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.