It would probably interfere with the compass if you have a 3G GPS model, but other than that not a problem.
The compass is primarily useful in navigation apps and the occasional educational or enhanced reality app like StarWalk. Those apps will try and adjust the information they display depending on which way you point the iPad.
So, if you are getting a 3G model I'd hold off on the magnetic clasp, at least until you have your iPad in hand, or you can confirm by testing or other users that the specific case you want doesn't interfere.