I really dont think this will cut down on 'capwhoring' at all, just annoy the players who legitimately use these vessels.
Myself for example - The only hogosha bases in the mod are the small-style stations, which my gunboat would end up unable to dock at. Likewise, hogosha can use up to battleship class vessels - so what if I chose a cruiser or Battleship as my faction flagship? I'd be unable to dock with any of my own faction's bases.
More restrictions like this arent going to help, capwhoring is something that needs to be handled in-RP by the faction leaders.