Planets used to fly out of orbit at high time steps in the first game. The threshold has improved in Universe Sandbox 2, but it can still have a tendency to glitch out at REALLY high time steps. The simulation has to reduce its accuracy to accommodate the higher speeds.
And yes, close orbits are more affected by the sim speed. I don't know what the "disappearing" planets/moons is about. I actually just tested a custom simulation at 50,000 year/sec and nothing went out of orbit or disappeared. However, I did make another one and the whole system became unstable and collapsed into the star, so maybe that's the "disappearing" you were referring to.
When you see the little clock icon next to the time step turn red, it means the simulation accuracy is reduced and it won't represent the orbits correctly, at least for the most part. Just take the simulation up to the point where it starts to become inaccurate, then leave it there. It shouldn't cause any orbits to become unstable. That should allow you to observe the system without becoming unstable.