Not my place to tell anybody what to do with their truck, but Issue 59 (the latest) of TDR provided some test numbers that showed that it is way more important to keep warm/hot under-hood air out of the induction system for the best useable power in these trucks. Yeah, the "Low Restriction", "Open Sided" BHAFs (Big Honkin Air Filters) look cool, but testing shows that any small gains from these setups is quickly lost and show a net loss over stock air boxes. Reason being that the motor much prefers cooler air from the fender (stock location) over hot, under-hood air. Cooler is way more efficient. Drilling out the box will actually result in a loss of power after things get warmed up. It's your truck, do what you want, but once you punch out the bottom of that box, you can't go back without spending some $$ and you will surely not get a gain in power. Your call, but the numbers are the numbers and you'll likely not get what you are hoping for. Good luck.
Byron