"What server" is not the subject of that question. 何がサーバーを shows that 何 is the subject and a/the server is the object, i.e., it means "What does/did do a/the server?".
I would say どのサーバーを使ってますか？ Another option might be どのサーバーでプレイしますか？ What server do you play on.
For you other question I would change the grammar of the sentence. "Who is from Japan" sounds awkward for some reason when translated into Japanese. I would say "Are there any Japanese here?" or "Is there anyone living in Japan here?"...