You called?
When I was talking about moving the fighter bays, that was really more about weapons than fighters going into it.
Supposing that the game engine worked basically the same way, but that the hangars were filled with subsystems that looked and took damage like (probably unshielded) fighters (and that their desctruction were somehow made significant in the mission), anti-cap beam weapons would be able to do serious damage if they hit inside. Other weapons, like the Fusion Mortar or Maxim, would also be able to cause big problems for the fighters.
The thing about sending a fighter into an enemy fighter bay is that it is full of fighters, and some of them are probably ready or very nearly ready to launch. You don't need to build a Terran Huge Turret or whatever, because you've already got a dozen or so fighters with several fighter-grade primary weapon systems (and some missiles, if the pilots don't mind a little collateral damage).
Of course, anyone who's seen that scene in Independence Day where the base gets raided (or heck, even in Tora! Tora! Tora!) knows that fighters can't respond at a moment's notice. If they got a fighter in, it would probably be able to take out a bunch of your fighters, and whatever defense you made (either with fighters or turrets) would not be able to save every last fighter. But it's probably more cost-effective to just shoot the things from a safe distance. Beams, 'lasers', and missiles--basically anything without the 'Bomb' flag--can't be shot down (although anything can be blocked by a bit of hull/asteroid/debris, in which case the beam has the slight advantage of not being an all-or-nothing weapon).
Really it's up to the person using the ship how to handle that potential vulnerability, if they even care about it. Fighter bays can be made destructible in the FSO engine, and it would definitely be possible to put little destructible fighters in the bays as well. Making the launching fighters replace the subsystem fighters, however, would be difficult. A shield mesh (or just a part of one, covering the front of the ship and any other crucial areas) could also be used to solve this problem.
As for hangar doors, I am sure they could be done. An easy way would be to just use a simple rotation (like window shutters (except just about all window shutters nowadays don't actually do anything, they just sit there and can't be closed if you wanted to)). If you're set on a translation, you could do something more like this:
|
| (hull)
|
\
\ (invisible subsystem, rotates around an axis where it touches the hull)
\
/
/ (another invisible subsystem, rotates around an axis at the end of the previous one,
/ same amount (or maybe doubled, not sure), but in the opposite direction)
|
| (hangar door)
|