If you increase the airfow you'll lean out the mixture, and newer carbed bikes run pretty lean as it is. I wouldn't expect it to take much to require a rejet, in fact it may help a bit anyway. If you're hesitant to get into the carburetor, I would advise against drilling the airbox.
Enough holes to make a difference in performance will require a rejet, few enough holes not to require a rejet won't be noticable.
However, if you want to drill it, go ahead, and get one of these-
Colortune Your Motorcycle
so you can see what to do to the carb. Changing jets isn't hard, but it'll take a bit of trial and error to get it dialed in just right.