On mine, I thought fresh air came in through the center of the filter and filtered air surrounds the outside of the filter. If so, holes in the can would bypass the filter altogether - not a good plan. But I'm just going off memory when I replaced it last. I may have it backwards.
I would also be throwing road slush up in there in the rain and possibly draw it in to the filter through the holes, and that may be a critical issue - Freightliner issued us a recall for the water drain than can plug and the plenum can fill with rain water and get drawn in for hydro-lock. The fix was simple, but I know it's a real concern.