To iterate on that, I'd love to see the ships in use by the Hegemony being stored at the station. You know how the fleets leave and dock at the station? Whenever that happens, the ships should physically disappear from the list, as they are now formed up in a roaming fleet, along with an appropiate number of crew and supplies. Weapons should also disappear from the list, as new ships are delivered, equipped with their armaments and then leave to go hunting. Ships that make it back in one piece should then re-appear in the station's inventory. In a way, one could simply buy out the Hegemony and deprive it of ships to use, giving it no, if not minimal presence in the system.
Now that would be awesome, would make the system seem more alive, rather than this strange personal reserve of ships and weapons that are just waiting to be bought up by the player.