Try to add these into shipdata.plist:
allows_auto_docking = yes;
allows_fast_docking = yes;
requires_docking_clearance = no;
Then into the
allow_docking = yes;
allow_launching = yes;
disallowed_docking_collides = no;
If you can dock then please locate if any of these lines can solve the problem alone also.
If still can not dock then maybe there is something in your savegame.
With only the first three added, Manual and Computer docking are still refused, but Computer fast docking works.
15:38:18.944 [LogEvents]: Player targeted Super Hub I 28037 who has 25000 energy
15:38:21.434 [LogEvents]: Player got message from Super Hub I 28037 : Docking clearance not required.
15:38:21.571 [LogEvents]: Player got message from Super Hub I 28037 : Negative. Your ship cannot dock here.
15:38:21.573 [LogEvents]: Player requested docking clearance and DOCKING_CLEARANCE_DENIED_NO_DOCKS
15:38:21.574 [StationDockControl_MFD]: Player docking request message: DOCKING_CLEARANCE_DENIED_NO_DOCKS
Gonna fly back in without clearance, now, to see whether docking works, without clearance. Nope, crashed. And not in a SuperHub auosave, but the one before that.
So now I'm going to go back into the package and fiddle with the various lines and report back afterwards,