@Rich.hIndeed, there would always be a criminal element in play. And post invasion resistance groups for example. Just because we defeated their army, doesn't mean we pacified them.
The reason I bring this up, is because logistics has always been a staple of strategy, for that reason we simulate supplies and civilian fleets. Due to the nature of JPs, natural choke points, there are very strategic opportunities to raid supply lines. The AI regularly sending its fleet to break on your front line defenses, and all your vulnerable supply and civilian ships are never in harms way.
I'd love to have physical ships but most implementations I know of, are extremely annoying whack em all. Usually some sort of militia\barbarian unit based on your current tech, that spawns in the "fog of war", that is either realistically weak and meaningless because the AI can't use it in a meaningful way; or unrealistic strong and disruptive without any way to avoid getting frakked by the RND in the first place (i'd hate to have to pave the galaxy with DSTS).
This is why I prefer the event compromise, its not as pretty but you'll suffer some of the effect of stretching your forces to thin without the added micro, performance overhead and silly AI scenarios.
@iceball3 Aurora simulate only specific strategic assets, but just because there are no commercial shipyard, doesn't mean that they aren't there. If we had TN materials, that make getting in orbit cheaper, not to speak of spaceflight and times, the system would be CRAWLING with civilian spacecraft and installations in FAR greater number than any navy assets we simulate.
And its not like you need a state of the art military battleship with combat pods to sabotage a freighter, especially on recently occupied frontier world. Any modified shuttle could do, or while in port just mask a bomb as space junk and throw it toward a hull for example.