The only modules that can run out of anything are the repair and carrier bay modules (for which you can see the remaining supplies on a particular module as a white bar under them).
That’s one of the reason why I don’t use carrier bay. You lose more HP from all those fighters flying to the edge, than the 600 you get per reinforced bay.
The same slot wasted on a carrier bay can used for a tractor beam.
The only race I use carrier bays with is the Tribe. They always have a few slots free that you’d usually be using for armour or shields so it’s not hard to give a good proportion of your cruisers carrier bays. The crew cost is high, but that’s always the case with the Tribe anyway and the carrier bay has the extra function of being a pretty decent HP sink. Spreading out the bays also means that you aren’t screwed if your dedicated carriers go down early.
The cost of a repair bay is not only a module slot/energy cost/crew cost/credit cost, but the 75% caution tag.
A fighter on the left edge is good as dead, so a 75% caution tag means taking away 75% of your fighters health. For tribe fighters with 40 hp, the caution tag just took away 30 of it. You need to use up 1 reinforced bay per 20 tribe fighters just to break even with the caution tag.
I always thought that for every x amount of fighters, a fighter bay somewhere in the fleet ought be required. Whether you use it or not during the battle, you can’t expect your pilots to sit in their fighters for days on end during travel to and from the battle!
It would lessen fighter spam and make for more interesting cruisers.
Still, I can imagine the fighters simply jumping in with the rest of the ships as they do now.
It forces the player to at least have one cruisers to use fighters, though I agree that’s a bad thing. All that does is put an engineless/weaponless carrier dummy in some corner.