Ships are, um, better.You have to have a variety though. If we threw out the defense structures that 'just shot lasers' because they are too normal, then that is not good at all. I would expect the kill-o-zap buildings to be just as useful as ships. And I don't see a reason to phase them out because 'ships are better'.
You can see which systems have ships from the galaxy screen. And they already do the job of kill-o-zapping, kind of redundant to introduce another element that performs the same function.
If you move into a system with no ships, there probably shouldn't be a battle. If you move a rook into an empty sqaure, there isn't an auto-battle with the square's "native defenders".