objects\cut\04906.pbd (the scene file for the Complex Hub) is updated in 04.cat. objects\v\10523.pbb is the actual model for the Complex Hub and doesn't appear to have been changed in any patch.
The files in the objects\stations\docks directory are the models/scenes for the individual docking structures. Why they put the Complex Hub in objects\cut and objects\v is something only the developers know and I don't really care about.

As far as I know, I'm the only person who has modified those two files, so there should be no other mods that have changed them.
What I could do instead of removing any of the docking arms is attach a third arm below the hub and put the capital ship dock there so the station would be able to handle: however many small ships the bay can hold, 20 TS/TP/M6, and a single M1/M2/TL
Doing it that way will definately cause any undocking cap ship to hit a bottom connection tube unless I make the dock accessible either from the side, or at an angle. The latter option might block the hanger when a ship is docked though.
I haven't even looked into it at all yet, but will see after work tonight.