Since I got bored arguing something that is a fact, I did the research...
Section 2. Drilling Specifications
a. Holes - The following limitations govern drilling holes in a bowling ball:
1. Holes or indentations, not to exceed five, for gripping purposes.
2. One hole for balance purposes, not to exceed 1-1/4 inch in diameter.
3. One (1) vent hole to each finger and/or thumb hole, not to exceed 1/4 inch in diameter.
4. One mill hole for inspection purposes, not to exceed 5/8 inch in diameter and 1/8 inch in depth.
AND...since the rule states that the holes are drilled for "gripping purpose," then OBVIOUSLY, if you drill a thumb hole (which would be for gripping purpose) and DON'T have your thumb in the hole, then you are violating Chapter 7 Section 2 Rule# A1.
Case closed!
Big Willy Style
PS...and by the way, if you drill a "weight hole" in the thumb area, to use at times, then you'd be violating Chapter 7 Section 2 Rule A2...since you'd then be using it for gripping purposes, and not for weight balancing...
PPS...edited for the link and spelling.....
http://www.bowl.com/rules/rulebook.aspx--------------------
Just my $0.02 so take it for what the Foreign Exchange values it at! 
"I was raised by a cup of coffee..."
***This message brought to you by the A.O.B.U.B.O.A. (Assembly Of Back-Up Bowlers Of America) which is now taking applications***
Honorary Member of the F.O.S. (and also the best back-up bowler the Saws have ever had)!
Visionary Test Staff Member '08-'09Edited on 8/20/2008 5:14 PM