I am a bit late to the party, but there is no reason to remove hangars from PDCs and they should absolutely NOT be removed. If you don't like them fine, don't use them, but don't snatch the option from those of us who like using them.
From my point of view, we have Mass drivers which can launch and recover huge masses of matter from space, I always just fluff that the same equipment is used to launch and recover TN ships and is built into hangars on PDCs to accommodate ships at least as large as the base can hold.
The TN ship drops into a gravity well and the base catches it and brings it safely into berthing, then when the ship is set to depart it is launched back into space, and once its free of the gravity well all its TN wizardry reactivates.
The same can easily apply for missiles and fighters to be flung into orbit where their TN properties become active.
As I said at the start, if you don't like it, or can't make it work in your own head, don't use it. Simple as that, the rest of us will think of ways for our universes to make it work within the existing technobabel.
Edit: as for shipyards and their crews. I always figured they were completely automated, which is why it took so long to retool the darned things to make a new kind of ship rather than just having them being able to build ships up to X size in whatever berth was available.
If your universe is allergic to automation (Something Aurora annoyingly is when it comes to ships already, my ships shouldn't NEED crew with the right components dangit! xD) then we already have telecommute robotics today. the workers sit on the ground and use VR to control machine in orbit to do the manufacturing. There, they are crewed, but the crew never has to leave the surface of their world or take their spouse and 2.5 kids and dogs to space with them.