Two Points
1) I can't think of any reason Decipher would object to the creation of such an index (as long as it didn't include any actual material from the books, but you knew that already).
2) If you use a database-type back end, you could easily output both a master index for all supplements as well as book specific indices. You could also output to multiple formats (like bookmars) with a minimum of fuss.
Jeff Tidball, Civilian | <a href="mailto:jeff@jefftidball.com">jeff@jefftidbal l.com</a> | <a href="http://www.jefftidball.com">www.jefftidball.com</a>