Actually, as far as I am aware that is how it is supposed to be: A vessel gains a bonus equal to the amount of other ships with at least one Turret in base contact with itself, up to a maximum of three. Because of that, the cases I used in my example (0 or 3 assisting vessels) are not really representative either. In a more realistic scenario, the most likely numbers are one or two for vessels with two Turrets (a pair or trio of Cruisers Squadroned together) and three for those with one Turret (Escort squadrons flying around with their members in hexagonal clusters of seven to optimally support each other). Against the Escorts the Bombers will indeed end up better off without both rules, but one or two bonus Turrets for the Cruiser will not actually hinder a wave of four at all. Four Attack Craft (2 Bombers + 2 Fighters) will create 5.33 Attack Runs against a two-Turret Cruiser with zero, one, or two Massed Turrets (but only 4.5 with three).
So my general conclusion for this would be that only Escorts got a significant defensive boost due to these rules being in place, which seems acceptable as nobody actually uses Bombers against them to begin with (only Assault Boats, against which they honestly deserved slightly more survivability to begin with).
The issue of incomplete waves arriving can be taken into account by comparing the amount of Launch Bays between yourself and the enemy, determining the ratio that can be taken down by enemy Fighters on the way and compensating for that with additional Attack Craft. I can't say anything solid about that though, as this is something between you and your opponent and I am not, in fact, a Psyker so I can't read your minds.

RayB,
Actually, your rules would still require the Turret Suppression rules, as removing them would make the dreaded Hive Ship and the Ork Hulk - as well as Nicassar Caravans and other Tau Orbitals with four Security Modules! - completely immune to Bombers as you would be incapable of causing any Attack Runs at all to a vessel with six Turrets of its own.