For what it’s worth, I adore your suggestion of carrier bays that will also re-load fighter weapons which use expendable ordnance. If this feature as well as Fighter Expendable Ordnance is added to the game, it will rejuvenate the rather drab existing state of fighter warfare.
The only one which does is the Parasites’ Cruiser Flak Cannon. Its area-of-effect damage is functionally identical to the spherical shockwaves produced by exploding warships. This type of weapons effect does not discriminate between friend or foe, and the Parasite weapon makes GSB rather “exciting” at times for your own fighters and frigates as well as those of the enemy. More than once, I’ve unintentionally done serious damage to my own light forces while firing at incoming fighter spam. Oh well, that’s how the cookie crumbles…
On a broader note, this entire topic is 100% “maybe in GSB 2” territory. I don’t dispute that the feature being discussed here is needed, but you’re not going to see it in the present game; Cliff has finished developing GSB 1 (Democracy 3 is Positech’s current project), so that metaphoric door is locked. At least Cliff has just today confirmed that he will be working on GSB 2 in the future, so there’s some hope for your fighter ideas. Good luck.