I believe the holes are for reduction of heat and probably should not be covered. I know that some have warnings not to put insulation within 6 inches of them.
Now, having said that, you can purchase covers that go over them - if you can get to them from above. I have some that can't be reached, except from in the room below. I actually removed them, wrapped the outside of them with duct tape, and reinstalled them because of a significant winter draft caused by them. I assume you have that problem as well?