It's definitely just more expensive for that specific case, but, well, making it more expensive is kind of the point. On the flip side of not caring about the replacement rate, you also don't care about the speed penalty, and the damage taken penalty doesn't seem huge in that case either - and if it is an issue, then the replacement rate is better, and that factors in too.
As far as larger ships, I *think* a higher cost for hullmod is probably warranted because fighters can add a lot of flexibility and act as a force multiplier for the ship; e.g. a wing of say Longbows is worth more on a ship with the firepower to back them up, etc. It kind of has to be a case of picking an optimal set of fighters for a ship to maximize the effectiveness, rather than slapping on any fighter being baseline-beneficial.
(It's hangar! Sorry; pet peeve.)
I'm not really sure; if the speed is decreased and the damage taken is increased, then I would think it would be less able to take evasive action to reduce the incoming damage, making it still more fragile. Though it is more the cost increase that seems excessive, currently I need 30 OP for the converted hangar and Xyphos wing, this gives me:
2 x Burst PD lasers (14 OP worth)
2 x Ion Beams (24 OP worth)
Alright, so looking at that a 50% increase isn't that bad and will bring it in line with the cost of the weapons they use (it feels expensive, but even these numbers are telling me that it isn't true). Well looks like I've taken the wind out of that argument, but there is still the remaining OP cost of the hangar itself (That hangar/hanger will take some getting used to, so I may accidentally swap in the 'e' at anytime, so I apologize in advance

).
In most cases I've noticed with hull-mods there is a pretty good explanation or buff for the increase in OP cost that comes with different sizes of ships. eg
-Blast Doors (more crew, bigger ship)
-Reinforced Bulkheads (bigger ship, more volume to cover)
-Integrated Target Unit (better range)
-Unstable Injector (bigger engines for a heavier ship)
-Hardened Shields (bigger shield emitter, more volume to encapsulate)
If the hangar's is identical whether it is on a Destroyer/Cruiser/Capital Ship, what is causing the additional OP cost?
All right I guess this is where game balance comes in (rather than rationalizing the changes with what you expect in reality or the rules of a made up one), and if I'm a bit more honest there are some hull-mods that do this (eg Expanded Missile Racks depends on ship size rather than how many missiles you are using).
Maybe you could apply a bonus depending on the size of the ship the hangar is installed on:
Destroyer: -33% speed, +50% damage taken
Cruiser: -22% speed, +33.3% damage taken
Capital: -11% speed, +16.6% damage taken
In any case I like the changes for the Apogee for the most part, I'll miss the damage a bit and I'm just a little lost as what to do with those medium energy mounts now (kind of almost wish they would just disappear all together so I don't have to think about it), but those amazing shields are still there so it's all good.
My Favourite Apogee configuration in 0.8.1a:
(BTW, do you generally round down or up in the case of fighter OP costs?, (15*1.5 = 22.5) 22 OP would still allow me to use this same configuration here by removing the Expanded Magazines, although I'll likely change this with the new weapon arcs...hmmm...however as a thought, expanded magazines would increase the Autopulse Laser to 45 projectiles now wouldn't it?)