They don't keep the space warm and they don't have to protect it in the winter months. Your only issue with an empty box below the cluster is mice which can be prevented with a mouse guard. You should be using mouse guards in your area.
I truly appreciate the feedback. Thanks.
I have read conflicting thoughts on this.Some suggest that if there is not a bee on every square inch that the excess boxes should be removed.
Conversely, I have read that it is useful to have dead air space below the hive. Well an unoccupied box seems to qualify as dead air space to me.
A local master beekeeper from my club told me to remove the box if it did not have any bees in it.
The lower entrance is set to the smallest opening and I am inclined to close it entirely (per Mr. Bush's approach). I know mice are quite the gymnasts and escape artists but I think the small upper entrance is too small for them. 7/8 by 5/16 inches. Let me know if those rascals can still get in. I do have a mouse guard that I can install.
https://www.mannlakeltd.com/10-frame-mouse-guard I could slip the horizontal tab between the top super and the shim to seal the upper entrance or screw it to the face of the hive and give the bees a ledge to land on , fan on, etc. I also have 1/8 hardware cloth on hand.