You won't be able to perceive anything "3D" if you're aiming for accuracy.

Even though we can perceive the "depth" of the stars through motion in this simulation, every star is still going to look equally far away, because their positions won't change between the left and right eyes. The same way we can't perceive the sun as further away than the moon -- depth perception merely tells us they're both "max far away".

You could always introduce depth perception by faking your eyes to be light-years apart, but of course that's not how it would really be in the spaceship...