I see your point but want to add something about Latin of this sentence. Actually, I think "Surely the university is not in Rome?" is the better translation for this sentence in English. To say "there is no university in Rome" in Latin, it would be better as "Nulla universitas Romae est". And for the question with num it would be like "Num nulla universitas Romae est?".
Surely there is no university in Rome? Surely there isn't a university in Rome? both make sense. But there is another possibility, it seems to me. Potentially Surely the university is not in Rome? expects the answer, No, you're right. It's in Padua - or somewhere else?