However, fighters aren't restricted from having bays themselves but that leads to weirdness where one fighter gets popped and half the wing dies
The fighter Schwarm (or whatever its name was) in older versions of the Neutrino mod had either this or those old drone ship systems. I think it was the latter since proper fighters before 0.8a were more like ships than weapons, and some ships had ship systems that spawned drones.
Before 0.8, some ships had point-defense drones as a ship system. For example, Gemini and Heron before 0.8a had machine-gun drones as a ship system. The Schwarm had a custom version that used copies of itself as a ship system.
Those drone systems have been replaced for standard ships (Astral has Recall Device instead of worthless laser drones), but I do not think those old systems cannot be modded back in somehow.