About 23 minutes into Episode 2 you get a real good look at them stowed onboard the sub (while being serviced, no less.) There are some sort of lift equipment to the ventral side as they're stowed, but I really can't tell if it's for the plane, or for the heatshields that are lowered for launch.
But there is a considerable amount of space where they're stored..sure, it's no hangar, but if they were simply on the sub to be launched, they wouldn't need to be any open space at all..just the tubes that they're launched from.
I believe the addition of drop tanks was a reaction to issues in the first skirmishes with the UN VF-0's, where they found themselves too quickly running out of fuel in the middle of a fight. Since this was (IIRC) the first combat deployment of the fighter (if not, it was certainly the first time it was fighting another variable fighter), it is within reason they did not forsee it to be as much of a problem as it became.
And I assume they were flying low on radar becausere they probably couldn't launch nearby, since UN forces were at that point expecting an attack, and presumably stepped up their CAP.