"Do you not have bananas?" is like "is it true that there are no bananas?". Then if there are bananas, the host can gleefully surprise you with them and feel like they solved a problem for you. This is only if it's said in a constantly upwardly-shifting tone, though.
It can be said another way, same words different tone, which sounds more like "how perplexing, there's no bananas, let me just make sure I didn't miss them because I thought they should be here". The host usually backs their answer up with an explanation of why there are no bananas.
A third form exists where it does sound accusatory. Like "you should have bananas you piece of crap". Usually said in a huffy puffy I-dont-have-time-for-this tone.
Maybe it also helps that all the sentence markers that make a sentence polite, negative, interrogative all get added on to the end (to the verb) in japanese, which probably makes the construction slightly less awkward. In this case it may go something like motsu (to have) -> mochimasu (to have, polite) -> mochimasen (to not have, polite) -> mochimasenka (to not have, polite, interrogative).
I'm making a lot of assumptions here though, I don't know if this is anywhere close to correct.
>"Do you not have X?"
In my head it sounds belligerent and accusatory. While the other form sounds polite.
This negative phrasing to induce a positive response, may be a Japan only thing?