I believe that the holes drilled into the boxes serve a number of purposes.
It adds to the ventialtion of the hive and helps with the curing process.
It allows access for the bees to different areas of the hive. Nectar foragers can access the honey supers, while pollen gathers can get to the brood nest.
This releaves some of the congestion in the hive and at the entrance.
It reduces travel time in the hive as well.
If your hive is set up with a bottom entrance the holes allow upper access. If you use an upper entrance, they will allow lower access.
But, as with alot of beekeeping practices, it is personal preference.
I've drilled some. I find the hole is always getting in the way of something I'm trying to do. If I had a bunch of corks that fit a standard sized hole in my supers, maybe this wouldn't be a problem, but I prefer to use a Imirie shim or a notched inner cover or a DE vent kit.
chris...i drill holes in my supers for ventilation but not 3/4" holes...a smaller 3/8" hole is sufficient. another tip...if you are using standard migatory covers you can shim the bottom three sides with lath (sides and back). this allows you in the summer to slide the cover forward and it will create a hidden vent...then in the winter slide it back and it will close the opening. this along with the drilled holes will create sufficient venting.
I have used a shallow super (which I also use as a top hive feeder to house inverted jars filled with syrup when needed) with one ~2.5" hole drilled on each of the 4 sides and covered them with #8 mesh. I placed this on the inner cover and the outer cover on top of it. I also use an open screened bottom board. The hive I am using this on was already "spilling" bees over the entrance on warm days. SInce I started using this I see much fewer bees at the entrance when warm. The inner cover has the notch exposed that serves as a small upper entrance this way.
The gentleman who introduced me to beekeeping was a big fan of holes, so it's not surprising I am too. I find just as many if not more bees accessing the hive through these holes than the bottom entrance. Rather than cork, I use corncob pieces to plug them up when it's time.
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