They are similar.
"Was it not obvious?" is unusual because it doesn't use the usual contracted form. The pronunciation is "Was it (pause) NOT (pause) OBVIOUS?" and shows extreme annoyance (..."you are SO STUPID ... was it NOT OBVIOUS? ..."
"Wasn't it obvious?" is usual. The pronunciation is "Wasn't it OBVIOUS?"and shows moderate annoyance (...PAY ATTENTION ... wasn't it OBVIOUS? ...)