On trello there is a post about this; this is just my take on what should be done in regards to fighters/drones.
1) you can allow the player to create their own drones/fighters in a building zone/mode for fighters/drones.
this would mean creating special parts for this build mode such as a fighter/drone reactor which powers things in a radius or wiring systems (as well as other parts). an a different save folder for fighter/drone designs and have the design minimize when it is spawned in so it actually looks like said fighter/drone
2) you don't necessarily need to have a special reactor as stated above what you could do is have a system where the fighter/drone returns to its mother ship when ever it needs to refuel/repair/rearm/repower
3) I heard @Walt likes the BSG style of special sections for take off and landing. personally I disagree an think there should just be one part that handles the take off and landing. granted it maybe easier graphically/etc. to have separate parts for the two functions.
4) I agree with the idea of having the ability to have more than one fighter bay an each fighter bay increasing the amount of fighters. the question is how much though? I think it should be 2 maybe 3 fighters per bay and the bay its self should be a 2 by 2. you could have multiple fighter bay sizes as well for example a 4 by 4 bay in addition to the 2 by 2 an a 1 by 2.
Edit:
5) you could also have a fighter/drone factory to replace lost fighters/drones and make it so it replaces them very slowly (say a fighter every half a minuet) to help prevent none stop swarming. or do this an have a fighter/drone factory cap per ship.