I think one of the reasons for the CAI and the K&N approach is to increase filter area that is drawing in air. The cone-shaped filter at the end of these systems has more surface area than the stock filter and therefore allows the intake to suck air through it easier. More filter area = less impedance plus it doesn't clog with microscopic dust as fast which also increases impedance.
Adding more holes to the stock boxes doesn't seem (to me) like it would allow your car to breath easier - you still have the same surface area on the intake filter... :alien: