Nuances. Your translation gives "who is it over there?" Which suggests that you may be looking at someone but you dont know his identity. Here it is more of a situation where you dont even see the person and you want to know who is there, not who the person is
누구입니까 comes from 이다 , a verb used for describing characteristics or quality like e.g. name, profession and so on.
거기에 누가 있어요 (from 있다) asks: who is located there. The difficulty is, that both totally different meanings are represented in English with the same verb 'to be'