Nope, it hits bases. I even made a scenario once based on this idea. It didn't actually use the spacial anamoly, since there was no way to control that. But the topic came up on the forum here, so I created a scenario where you had only a base space yard transported to the middle of a nebulae in a quadrant where you had no other planets or ships. You had to build troop ships and take over an AI planet and build your empire from there.
I had a spacial anamoly hit a mothballed ship once. Hows that for useless?
And it even affects units. I had a satellite once that got transported accross the quadrant. It was sort of useful though since it allowed me to make contact with another race and start trading with them.