They hide anything under them from the local map. If you have a secret half of your level, and you dont want the player to see it by looking at their map, put a black plane over it.
Wow, did not know that, thanks! I was wondering why some places had them facing upwards but weren't even where the PC and NPC's can go...
Otherwise I use them to cover things up that I do not want to be seen and should remain dark, you just have to get the positioning correct. For example a well with a long shaft downwards, if you place one on a tile you can still see part of the tile when you look in the well. It would be good if there was also a round one though.