I have been using mid and upper level entrances for years.  I drill one ¾ inch hole just under the front facing hand-hold on EVERY box. They are drilled during assembly at about a 45-degree angle with the downward slope to the outside to prevent rain-in.  The exposed surface inside the holes is painted along with the rest of the box. I have never experienced any advanced box rot because of this hole. The bees use them religiously. 
It is only my theory based on observed traffic flow, but I believe they add efficiency.  During the flow, foragers are using the holes in the honey supers.  This prevents them or the house bees from traversing the entire hive (and excluder if used) to store honey in upper supers. This would also reduce the traffic through the brood rearing areas. Reasoning would lead one to think this out, but this is not based on any scientific theory.
Another benefit with holes is not compromising any bee space dimensions such as I experienced with a shim and resulting in burr comb. The shim, by the way is another piece of equipment I do not have to store or keep track of.  I manage these drilled openings with wine bottle corks or corn-cobs.  If I want to reduce entrance options or block cold air in a certain box, I plug it.
On a cool morning here in Ohio I have seen vapor pouring out of these holes when the bees are evaporating nectar or syrup.

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