*Sesquipedalian sights his friend Cuttenslise*
Fire Control, acquire lock on target. Warm up the Welcome Beam, and... FIRE!
Exits are to the sides and rear. In case of emergency, flamethowers are located beneath your seat. If a large hungry Shivan jumps you, its probably just Carl. Give him your lunch and he'll go away happy.
Anyway, it's good to see you. We'll be getting our own forum here in the next day or two for SA.
As for your question, that actually pretty easy to solve.

In your ships.tbl, and find the entry of the ship you want to change. In the entry, find the line (or lines) that look like this:
$Subsystem: fighterbay01, 0,0.0
and change the first number after the subsystem name to a positive value. This value represents what percentage of the ship's hit points the subsystem has. Following FS precedent, one might change the above line to:
$Subsystem: fighterbay01, 5,0.0
Your fighterbays will now take damage (though for some reason they won't show a percent left on the HUD target box like other subsystems) and can even be destroyed.