"Isn't it short?"
Is not it short? Is it not short? Isnt it usually means "it is, right?"
"Isn't it short?" is fine. It can be used to imply that something is positive, as you point out, but it can also be used to just ask whether something is not short as a simple question.
"Is it not short?" would probably be the closest. Not to confuse you, but it depends on the intonation. If a simple question it would mean 'Is it not short'?, but if asked in an incredulous tone it would mean 'It's short, isn't it?". The same could be said for the same phrase in English, depending on whether you emphasize the 'it's short' or the 'isn't it'.
"It's short, right?" would be 「みじかいでしょうか？」or similar variants.