There we are again with the differences between Hungarian and English. :D
"Ott várok, ahol te vagy" is a proper sentence, but it's not saying what the Hungarian sentence above is saying. It says, "I wait where you are, hang around, right in this moment." (And that's also the first thing I think about when reading the English translation, so I can't blame you.)
"Ott várok, ahol te", on the other hand, uses the same verb for both clauses, so it's actually "I wait where you are waiting", and you can expand it to "Ott várok, ahol te vársz." Using the verb twice is alright, but not necessary.