I wouldn't cover it. Even though set to not wake up on anything, it could still wake up, keep on running. It could wake and panic or hang in an unworking state but still generatimng heat. And that would not be healthy with a cover on top of it.
If I was away from home like a month, or a year or something, that's different. I would unplug it and put to closet, or cover with a towel etc.
Dust seems to accumulate mostly vertically, on horizontal flat surfaces. The top plate of the 6,1 "core" gets dusty pretty quickly. Still I don't think dust makes it way that much on the sides of cylinder, to the inner computer parts.
I think the dust in there, inside the Mac, is mostly due to ventilation, and it comes in with the incoming, sucked in air from bottom.
edit. maybe I read the question too hastily. Sometimes the fan runs when in sleep, I guess it's doing the background tasks allowed in system prefs or something. Again, one reason more to not cover it.