My old 321s developed small cracks at the valve hole after being drilled out for shrader. To be honest it never really affected anything though, I still rode the rims without problems for a couple seasons until that bike got stolen. That being said if I had a new set of those rims I wouldn't do it. What's wrong with presta?
On a related note, the new 729s come shrader drilled with a plastic adapter for presta. These don't seem to crack and I think it's for the reason LIPS stated.