Did some quick research. Only took me about 20 minutes to get it all done. In it's entire history, the NCAA has vacated only 8 championships (that I could discern from their website). The hall of shame:

1989-Div. II Football-Mississippi College
1988-Div. I Women's Golf-Tulsa
1990-Div. I Men's Lacrosse-Syracuse
1971-Div. I Men's Soccer-Howard
1978-Div. I Men's Soccer-San Francisco
1995-Div. I Softball-UCLA
2002-Men's Volleyball-Hawaii
2003-Men's Volleyball-Lewis

You'll see the latest vacation of a championship was the 2003 Men's VB championship Lewis got stripped of. It doesn't happen often, but championship vacations do happen.