I've seen a couple of racers put holes on the inner sidewalls, but only if it's going to be dry conditions.

Personally, I put them in the center of the tread, so that any water that gets in the tire from running, or even cleaning them, will work its way out.

I typically do three holes, spaced evenly around the outside (about every 120 degrees). I use a leather punch, and the hole size is a tick smaller than 1/8". I believe it's the third one up from smallest.