"Shouldn't it be" is correct for all situations other than extremely formal writing. It would be used to start a question -- "Shouldn't it be blue rather than orange?"
"Should not it be" is also correct, but sounds really awkward and old fashioned. You would more likely use "If it were not blue but orange, "
"Should it not be" means the same thing. It forms a start to a hypothetical with the same meaning as "If it were not blue, I would not like it."
"Should it be not" is also very archaic sounding but correct. The meaning is a little different, though. It also forms the start to a hypothetical like "Should it be not blue but orange, I would not like it" That's very awkward sounding too. You would more likely use "If it were blue rather than orange..."