Yes, it can harm the game: sometimes the interface does dim the asteroid/planet, making it difficult to navigate and build. Furthermore ships may have to fly into the wrong direction, make a 180 degree turn and then jump in order to reach the overlapping region.
Sometimes it's so bad that two such things overlap directly. In that case it is impossible to control the ships or build anything properly.
The bug has been reported, save files have been sent but the case is being ignored by tech support.
Screet