Ideas:
CV goes into an automatic holding pattern at it's current location when port is destroyed. Eh, seems silly.
CV is slowed down by 10% when home port is destroyed. Thinking along the lines of conserving fuel because resupply is... alright forget that one.
CV is visible on clipboard after X hours have elapsed while its port belongs to someone else. <-- I think I like this one.
EDIT: Read Babalonian's link. Pretend this is a comment on hiding CV's in general.