I've never seen a shop missing an item that I had bought before a reload though. It doesn't feel like other shops. The same supposedly unique item was also in stock twice, though maybe the modder didn't make it unique by accident.
Well, Bethesda usually just did it for small things like ingredients, beginner weapons, clothes... so you wouldn't really notice unless you were really paying attention.
Tealpanda used quite a large selection of Leveled Lists for her shop, so it's much more noticeable when unique items aren't there, and also creates the chance that the same item will reappear even after you buy it.