At full throttle, the air coming off the flywheel is shoved into the air box. I'm no engineer, but it would behoove engineers to keep positive pressure in the air box from the flywheel air to keep from junk entering the air box through other openings.
I know on my Stihl saws, there are centrifugal separators that keeps most of the junk out of the air box, but allows air from the flywheel to pressurize the air box. I'm guessing this isn't true on all saws.
So really, it depends on the saw whether or not cutting extra holes in the air box is a good or bad idea.