In "Comment tu t'appelles ?" there is also two "tu". The "t'" is also a "tu".
"s'appeller" is a pronominal verb. So we need to put a pronoun.
"Comment vous vous appelez ?" or "Comment vous appelez-vous ?" is like "How do you call youyourself ?" in english. And as you can see, in this question, you can find two "you".