I think; like a lot of us here; that empty stations should not be that easily accessible. The use of the most important one, in faction controlled system, could be link to specific quest as stated previously. But I would thing the use of STORY POINT could be interesting here.
Cleaning up and actually finding a way into the storage facilities of an old rusty space construct should be reserved to experienced spacefarer. Story Point are the gameplay equivalent of some kind of savoir faire and have an obvious role to play here. Going further, because making use of a derelict base is a little bit more work than just using good charisma or engaging a daring evading manoeuvre I think the SP cost of unloaking acces to free storage space should be coupled with the one time use of a specific numbers of CREWs, MARINEs, and SUPPLIES in a way similar to colonisation. Because, obviously, to guard and manage all your precious cargo you would need some kind of human operation going on.
The acces to item storage and ship storage could even be dissociated, requiring two specific one-time investment from the player to unlock free storage: again, storing some cargos and dissimulating huge spacecrafts is not the same thing. This will also build a sense of clear progression for the player.
The icing on the cake: pirate fleet could be spawned orbiting the station with a strenght relative to the value of the stored items. The player should then be forced to either sneak or fight this moderate threat to get acces to his belonging, provinding fun and meaningfull gameplay encounter but also emphasing the need for a real colony base.