Ok, after some determination not to give up on my game, I almost found a workaround. Maybe it will help the devs troubleshoot...
Building a new hangar at the affected bases has made the game "see" the *old*, occupied hangars.
For instance, at one base I have 4 hangars originally with 1 Marauder, 2 Foxtrots, and 1 Condor. I decommissioned the Condor (game was already missing the hangars but I could still click through the aircraft) to make room for a new Marauder transferred from my main base. Then I built a new hangar there. After the completion of the new hangar, I can now see 3 hangars on the Aircraft screen for that base: the ones with the Foxtrots and Marauder in them. The empty former-Condor hangar and the newly built hangar still don't show up, and I still can't transfer from main base.
Then I just tried decommissioning one of the Foxtrots there to see if I could transfer the Marauder. The empty hangar immediately does not show up on Aircraft screen and I still can't transfer the Marauder.
I have a few save games made through various stages of this process if examining them would help debugging.
Finally, just want to mention that this didn't seem to start happening until I returned from a ground mission at a crashed Carrier. Or at least that was when I first noticed it, because I then had enough Alenium to make another Marauder. I hadn't transferred any planes within the last few game weeks, so its possible it started sooner. But prior to that I was doing a lot of plane shuffling while upgrading my fleet.
