We have Ninja bases now?
Enemy bases (I have mercs, academy and guild, so I assume all bases are the same) now have a visible radar circle, a rather small one. When you pass through you are being attacked. It seems to take some time to regenerate the fighter, after shooting it down I could pass through the radar range for at least a couple of hours, maybe even longer. So send a proper fighter, then attack the base/supply ship with your transport (ideally parked nearby).
You have to be careful, because on the way back from a tactical mission you cannot change course. (maybe you can transfer to another base? Haven't tried.)