Oh, that. The dark stuff is practically night. Things are only "hidden" in night areas when they have no lights, but the area is not completely black. You can still see details (terrain, units, buildings) if you look closely.
And some more OP 3D feature Requesting!
Functions that return useful numbers, such as no. of unoccupied Scientists, no. of unoccupied Workers, Unused Power, net Food Production and the likes.