Qual è la differenza tra レストランは、どこですか？ e レストランは、どこにありますか？ ?Sentiti libero di rispondere con un esempio.

レストランはどこですか？
レストランはどこにありますか？
(No 「、」is needed for the sentence is so short.)

Although they basically are the same, the former sounds too direct to me. Too direct and short so that I might get sort of lost which answer I should give if somebody asks me that question. In that sense, the latter sounds more natural.

Also, I wan not quite sure about by saying 「レストラン」 do you mean a general place to eat or you are trying to find the location of a specific restaurant? I get the feeling that you are talking about any restaurant. If so, then the question works fine.