Firstly, "Is it not a nice day?" is a proper use of English, although it is often contracted to "Isn't it a nice day?" (note the change in word order).
Secondly, this structure is called a Negative Question. Such questions are used:
- a) to express surprise:
"Isn't it ready yet? You've had four days to do it."
b) when we expect a positive response:
"Isn't it delicious?"
c) to contradict a previous statement (politely):
"Is it not spelt with a y?"
- Haven't we met somewhere? / Have we not met somewhere?
Don't you like it? / Do you not like it?
Shouldn't we go now? / Should we not go now?
Won't she have finished? / Will she not have finished?
Aren't you being provocative? / Are you not being provocative?