On my 06 Classic that has cats, I drilled straight into the final pipe which resulted in a sort of oblong hole in the pipe on one side since the final pipe comes out at an angle.
Wound up with a hole that was 1/2" wide(largest drill bit I had) and maybe an inch long.
Resulting sound is a heck of a lot better that the three hole mod. Deeper, not as raspy!
I have since put on a set of BUB Big Willy pipes that I purchased used for cheap and they sound fantastic! Nice, throaty tone and not obnoxious as long as the baffles are in place.