Tests have shown that there is almost no difference in run time. (A few minutes at most which is a statistically meaningless aberration given the runtimes involved.) Performance, on the other hand, is noticably better.
I'd say your main concern should be the warranty which will will no longer exist after you've totally disassembled and reassembled the entire machine. 🙂 That's why I tell people to get the 60 gig drive upgrade when they buy an ibook. And bluetooth.