@Sig,
I totally agree with you. Ugh, a lot of the HA documents feel like someones wishlist, chaos doesn't need tons of upgrades, and already has a way to represent every 'mark'. The ships should at best be 'named' ships from the despoiler/desolator stat. Also weren't there only 3 despoilers built?
The same way I feel about orks, I don't get why there is such a need for 'marks'. Each clan just has preferences, and each one can be represented in the current ruleset, (ie. deathskulls taking looted torps).
The extra two chaos vessels, the Hecate and Emasculator. Well... the Emasculator is a lance Murder, Carnage style, it is pointless and would make people want to take Murders less (which the lance option was a large reason for taking them). The Hecate doesn't seem to have any serious point either, it feels like a 'just cause' ship.
The Chaos Space Hulk, I hate to say it, but I don't see chaos ever making use of one. Unlike Orks who would probably ride a moon around the galaxy if they could strap large enough rockets to it, chaos worshippers are human, and would likely remanufacture the hulked ships inside instead.
The vessel certainly exists in the fluff, like The Soul Drinkers Brokenback, but I think that this would be something you only play in fun games or on your own.