How important is intersecting geometry?

Working on a space battle. Some of the ships I have modelled are really clean topology so no overlapping shapes. But some other ships I whacked together more quickly and overlapped shapes. Obviously the quicker way would be more preferential, but how much does it matter if shapes overlap?

it shouldn’t matter at all, as long as it looks ok. it is typical to use many different pieces for a spaceship.

forgot to mention this is for animation, dunno if that would matter.