Wouldn't a white ship against black 'pop out' even more?
What the hell does the color of the background have to do with the 3D effect?
Technically having any flat color in the background will not work as well as a background with a pattern or noise. Shots with much more frame of reference or depth work a lot better.
The 3D effect solely results from stereoscopic vision. The background has nothing to do with it. You are right that there's not much of a 3D effect in space battles, but for the wrong reason. The right reason is that human eyes are only 6-8 centimeters apart, but a spaceship in Star Trek is 300 meters long. If it fills the whole frame, the difference between both images for the right and the left eye are minor. Thus, the 3D effect is barely noticable.
Which is for example why physical miniature shoots in 3D are 'problematic'. You can tell much easier that the scale is off in 3D.