I've done it both ways. Obviously if anything in the diff has failed, you need to put new bearings in or it is very likely you will be doing it again very soon. Also, probably a good idea if the car has a lot of miles on it, just because you are there. However I have done plenty of gear swaps on cars under 100K miles, and as long as there isn't any pitting or discoloration, there's no reason you can't re-use the bearings.