Okay, so today I set my freelancer up, got in my stalk and flew around aimlessly for a while. Then I sat on a base reading news and stuff, trying to figure out what's changed in the recent update. Then I saw 2 new hardpoints on my Transport.
One was caller "carrier bay" and the the other one was called equipment type 1 or something.
Docking Bays are useless for now, as plugin was disabled due to it causing some trouble with server. Unless something has missed my eye and they are re-enabled.