Comment by quelltext

This is as usual not universal.

First, in shops people clearly ask for whether they have something.

It's super common for clothes and shoes stores to have more sizes in the back. I might ask the negative form when I think it's likely they don't have the size for a reason, e.g. if the same shirt in a different color is laid out in my size. "You don't have this one in XS (like that other one here)?"

In situations where you expect a product to be stocked right there in its usual place but it's not there it's natural to ask in the negative. Ex: bakery that usually has a full tray of croissants has an empty one / or none at all. If you can guess it it's also natural to ask specifically if they sold out.

In situations where it's not clear if a shop even has a certain product / size or if you cannot find one and you are looking, it's definitely not unexpected to ask positively. Ex: Asking whether a different option is available, or a different flavour than the one you see in front of you, or "do you have this particular vinyl from ...?" (it would be super odd to ask negatively in that last case).

Often actually both work and choosing the negative form IMO is harder to get right.

There isn't really an inappropriateness component, and frankly the clerk in your example either was rude or they simply said "if it's not on this shelf, we unfortunately don't have it". And to be honest, I don't see how their response would have been different if you had asked negatively.

Maybe if you said "You don't have this, right?" the clerk would have said "that's right", but in general, if you ask "do you have" vs. "do you not have" should almost always result in the same apology that unfortunately they don't.