Both are correct, depending on the situation. In the first sentence, it is understood that the person is going to visit Japan. In the second sentence, the person may or may not visit Japan in the future - we don't know.

"You must visit Kyoto..." this is a strong recommendation. "...when you come to Japan." = the trip to Japan is definite. "...if you come to Japan." = the trip to Japan is possible, maybe likely, but not definite.