Well, fundamentally the situation is similar in a crew. Each crewmember has specific aptitudes and a few notable friends/lovers/enemies. But there are also a few differences between CK2 and this.
One is that none of the characters are kings. The captain of a starship or even the admiral of a whole fleet isn't a king. It doesn't make sense to simulate random non-player characters on other ships, since their behavior doesn't affect the universe much.
There is a question about the nature of civilization in general. I don't think it makes much sense to even simulate a space nation in this kind of game. Instead, it makes more sense to drive all of this using opportunistic role-filling.
For example, the game rolls up a mission opportunity. You see that there is a medical mission. The type and severity and all of that are algorithmically determined, and then the game simply slots in the major actors, usually people and factions you have met before.
The pirate captain that escaped two months ago is back - not because she was simulated into the scenario, but because she's in our bank of available characters. This time she's one of the ones being affected by the plague, not a villain like she was last time. The affected world is... BX9, a world we scanned a few months ago. Etc, etc.
There is room for some simulation, but it'd be over the course of the mission rather than in the spaces between missions. The pirate captain doesn't really exist unless she's part of a mission. BX9 doesn't exist unless it's part of a mission. I mean, you could go hunt these people and places down, maybe, but they're not being simulated until something like that happens.
How things unfold once the stage is set, that would involve some simulation. There are opportunities in that. For example, the pirate captain is a pirate, even though she's on the planet's side today. That could result in tensions. As you work away at your medical mission, the tension rises and, unless you take on a mission to lower that stress, it could explode as the pirate captain decides to just take over the planet.
But that stuff is still hazy. As actors go, it's important to realize that the "off stage" characters, places, and things are simply gone. They're not simulated at all. Instead, they're just pulled into the missions as slots become available, and some tenuous backstory explaining why is slapped in automatically.
(This also makes sharing them/syncing universe states between players really easy.)