It doesnt hurt as long as you jet it accordingly and use other protection depending on your riding style.
If you add a exhaust to let more air out then you need to let more air in. Hence remove lid and add high flow filter. When doing that you need to add more fuel to the mix to keep the bike running strong. Depending on your riding conditions you may need a outerwears cover (doesnt hurt regardless of conditions) or a after market lid. People that usually drill holes do this to add a little protection back over completely removing the lid. :thumbsup:
Well, you'll ruin your lid. If you do any sort of riding through deep creeks, I would strongly recommend against that. That lid is designed to keep water out. Unfortunately, I'm unable to drill holes in my lid as I ride through entirely too many deep creeks on a normal ride..... So, just make sure it suits your riding style if you're gonna do it.
I wouldn't drill them. That's about what I do, but there's times you hit a little deeper spot like up to the seat. If you're in lots of water don't do it. It's not worth it. You're not on a motocross track. lol.