There's a lot to think about here.
1) "Battle Barges" and "Strike Cruisers" such as they're fielded in the M41 fleets are the product of a reorganization of the Space Marine military forces from a fleet-based conquest oriented force (apply the maximum available force to a planetary target, eliminate resistance, move on), to a brushfire war/defensive force (respond to crisis, fight through potentially hostile orbital environment, deploy troops to the surface immediately, and either stay in low orbit to provide fire support if orbital supremacy is obtain(ed/able), or pull out and play cat & mouse until the Imperial Navy arrives to establish orbital supremacy). As a consequence, we have light cruisers and battleships that are stripped down to their absolute minimum in terms of conventional armaments before being bulked up with extra armor, hangar space, and engines.
2) My assumption is that a modern strike cruiser can comfortably fit more than 100 space marines, probably closer to 200 if they're willing to get cramped, in order to fit auxiliary forces (scouts, terminators, air & ground vehicle crew, chapter fleet staff).
3) I've read the same thing about battle barges somewhere, that they can deploy up to 3 companies simultaneously, which pretty reliably sets their carrying capacity to at least 300 marines, if not more like 400-500 if we're factoring in additional room for auxiliary forces and support staff beyond chapter serfs.
4) I'd assume you could comfortably billet 10-20 marines on a frigate somewhere, mostly because they're really just taking up some minor cargo hold space while being transported to a warzone on what is a higher-tech, lower crew requirement vessel. You could probably fit a Storm Eagle or a Storm Raven into a ship's cargo lighter bay, and there's your surface transport for a small strike force.
Now, the Great Crusade era is a whole different matter.
1) Imperial High Command pretty much went like this: Emperor/Malcador > Primarchs > Legion Praetors > Legion Captains > unaugmented human officers (navy/army). Under these circumstances, Space Marines were posted on Imperial naval warships ranging from frigates to battleships (and stuff that probably exceeded that scale classification too).
2) From as far back as the Realm of Chaos book and 1st Ed. Space Marine the Eisenstein was a Crusade-era frigate, on which Capts. Garro and Grulgor each had roughly a company's worth of men aboard. That right there throws our manageable billeting dimensions right out the window.
3) We presumably have marines billeted on light cruisers, cruisers, heavy cruisers, grand cruisers, and battleships throughout the Crusade fleet, anywhere space can be made to billet a company or more of marines on a ship that has the capacity to deploy them (presumably in company strength, but not necessarily, especially if it's a reserve company on a dedicated gunboat).
4) In the stories, the Vengeful Spirit not only billeted an unknown number of Sons of Horus, but it also had room and deployment facilities for at least two Emperor-class Titans, and the Conqueror has facilities for an entire Titan Legion of Warhounds, so based on that lore information, and lacking anything to contradict it, we can safely assume that the 2010FAQ rules for those two ships are underpowered, and the technical displacement characteristics of a Gloriana-class Battleship are "fucking massive" by "dear god, how does this thing turn without tearing itself in two?" I'd venture that Crusade Fleet flagships, if they're Gloriana-class (and we can probably assume there were at least 20 of these, at least one for each Legion), can probably hold at least one if not more Chapters' worth of Legionaries, not to mention support vehicles, Imperial Army auxiliaries and a Titan battlegroup of some size. I'm just going to ignore Abyss-class ships for now.
5) In terms of deployment, a ship's ability to deploy whatever Marines are onboard will have less to do with the number of Marines present, and more to do with how large the launch bay and drop pod facilities are. I figure it's pretty safe to decouple marine carrying capacity from simultaneous deployment capacity regardless of whether we're talking Crusade-era or M41-era, especially since we are dealing with kilometers-long warships (even if they are 25-33% engineering and thrust).
So I guess the question is, what assumptions do you/we want to work with?
If we take the Eisenstein as an example, we have more than enough room for 140-200 marines to have a running gun battle across several decks while in warp transit, with the crew largely uninvolved in the process (aside from the poor saps on the gun deck where Garro and company really laid into each other).
Based on that, we can extrapolate that a light cruiser (strike cruiser or otherwise) could easily fit 200 marines, probably closer to double that amount, and anything from there (standard cruiser hulls, grand cruisers, battleships, super-battleships/dreadnoughts/warships the size of small moons) gets really out of whack.
I guess a related consideration would be how much of the Imperial Army was carried on dedicated troopships, and how much of it was also carried on active duty warships? To my knowledge (and brief dive through the novels), there's no real estimate anywhere. As another example of flexible billeting space, we have the Raven Guard cruiser Avenger, which carried a company of Raven Guard, a regiment of the Therion Cohorts, and the 3,000 Raven Guard evacuees from Isstvan V. In this case we can probably assume that things were severely cramped on board the ship on the return trip, but it was managed. We also don't know what "size" cruiser the Avenger was (light, cruiser/heavy, grand).
So... where to start?
I figure:
1) We can either accept or reject the Black Library soldier-to-ship ratios.
2) We can accept the Epic: Armageddon deployment numbers (100 & 300 respectively) as billeting numbers, or not. (I'm inclined to decouple deployment and billeting for the reasons stated above, and also because Epic tends to streamline things for balance purposes too. See: Thunderbolt Fighter)
3) If we accept the ratios, we may need to do so flexibly (make the Avenger a grand cruiser, for example).
4) If we reject the ratios... we're back to square one, with no real idea beyond anecdotal evidence in some of the lore as to how many Marines a modern strike cruiser or battle barge can deploy, taking into consideration that the Crusade-era fleet probably didn't have/use such ships, or had some vessels specialized for that purpose within larger fleets containing a full spectrum of craft controlled by each Legion.
Based on the Black Library novels, each Legion was either broken up into smaller fighting forces and scattered across numerous Crusade Fleets (anything from chapter to company size), or kept together and wielded like a massive sledgehammer (Death Guard, a significant portion of the Luna Wolves/Sons of Horus). Granted, my example of the Sons of Horus really revolves around the fact that we spend most of the novels in the command battlegroup, following the Vengeful Spirit and its attendant fleet.
I would assume that a Crusade Fleet task force probably consisted of 1-2 battleships,1-2 squadrons of cruisers, and a suitable number of escorts (a.k.a., a 1500-2000 point BFG fleet). It would make logical sense to build exploration fleets around a battleship, 3-6 cruisers, and their attendant escorts, and then where necessary combine these task forces into larger fleets where serious opposition was found. The Legion command fleets probably consisted of the Legion's flagship (a Gloriana-class), several attendant battleships, and proportionate numbers of cruisers and escorts, serving as a vanguard fleet when entering a new sector, or as a roving reserve that could apply a sledgehammer to a particularly recalcitrant nail where necessary. Back to my suggestion of a standardized task force building block for the Crusade Fleets. Assuming a battleship and half a dozen cruisers, I would figure the Legions would be billeted on the battleship and any dedicated carriers (i.e., the vessels with sufficient launch bay and lighter bay capacity to deploy marines in company strength or greater simultaneously). Imperial Army forces would probably be billeted on the remaining cruisers, or/as well as on dedicated troop ships attached to the task forces.
If I were Dorn or Guilliman, I would probably assign a Chapter to each task force, to be distributed across the vessels capable of landing the Legionnaires in company strength. This is probably way below maximum carrying capacity, but the fleets in the novel are depicted as truly massive, so I figure it's probably not unreasonable to have 1000 marines plus an unknown number of Imperial Army regiments (and possibly Titan support, although with notable exceptions these were probably based separately on Mechanicus vessels and/or roving Mechanicus reserve fleets, reponding to requests for reinforcement as needed) assigned battleship/grand cruiser and attendant cruisers. That would put a 100,000 strong Legion at roughly 100 battleships, 600 cruisers or so, and let's not think about the number of frigates and destroyers. This seems a little extreme, but the depictions of the naval battle at Phall discusses dozens of ships tearing each other apart between the Imperial Fist and Iron Warriors fleets, and there's no indication that Pollux took the majority of the Imperial Fist fleet with him, just as massive a fleet as could be spared for a reprisal force, whatever that is quantitatively.
I know I'm making a lot of assumptions here, but since that's about all we can do, feel free to question/challenge them. This is just my first pass at guestimating based on the lore I've absorbed along the way.
