That's because N-body physics implies unstable orbits. For the planet scale objects, the game designers would have to make sure that the orbits don't go crazy

That's because N-body physics implies unstable orbits. For the planet scale objects, the game designers would have to make sure that the orbits don't go crazy (over times that can be explored at maximum time warp). But then if the goal is to keep those orbits stable, why not just save all the dev effort and just keep them on Keplerian rails? For the smaller objects launched by the player, unstable orbits aren't necessarily desirable either. Imagine going on a multi-decade mission and returning home to find your favorite space station missing. Game devs aren't going to spend effort on complicated features that will just piss off most players.