If you build a starbase in one of the uncolonisable gravwells (ion storms?) where all fighters and bombers are grounded, the base's squadrons operate normally. While it's fun stuffing a starbase to the gills with bombers squadrons and having them zoom about unchallenged, (no enemy fighters to worry about and no enemy bombers to counter) I think this might be not quite as intended. 
(This was with an Advent starbase by the way, don't know about the others)
