계시다 is the honorific version of 있다. Right. But in this sentence 선생님, 이번 주말에 시간이 계십니까?, you are using honorifics to 시간. 시간 is not the person that you have to use honorifics. 선생님 is the person that you have to use honorifics. You have to use honorifics to 선생님. So you are using the honorifics ~십니까 in this sentence 선생님, 이번 주말에 시간이 있으십니까?