You can rate all magic items, as a group or per type, as one of three levels of difficulty to make:
- Impossible -- made by gods, lost magic, or unique situations, like a holy relic or legendary artifact.
- Difficult -- takes a lot of time, effort, and materials to make, much like a work of art.
- Easy -- takes little time, effort, and materials to make, much like a crafted item.
How magic items are sold or should be sold depends on the difficulty rating.
Impossible to make items, like relics, get sold through brokered deals -- unless they're stolen, in which case the sale is still essentially a brokered deal. If there are, say, a thousand flame-knives, there might actually be a trader who specializes in flame knives, although that's probably not the trader's sole commercial interest; you won't find a "flame-knife store".
Difficult to make items, like works of art, are made on commission or as a labor of love, but might be brokered for resale; collectors may be willing to sell pieces of their collection, and in a large city, you might find a collector with enough items who operates what might be considered a magic "shop", although it functions more like a gallery. Otherwise, the only merchants who sell magic items are those who have one or two magical versions of a common item they sell, like a rug merchant who just happens to have one or two flying carpets.
Easy to make items might actually be available at a permanent location. I'm personally leery of dedicated shops of any kind, let alone magic shops, patterned after modern shops, except in deliberately silly settings or urban fantasy settings. Instead, most towns will have a marketplace where a scribe could sell a few scrolls of protection, or you might find some cantrip wands for sale. Some frontier towns may have a general store or trading post instead of a weekly or daily market, operating more on wild west model. Merchants who specialize in given items might have dedicated shops in the largest cities, and might have a magical version or three of their specialty item, but otherwise, you go to a craftsman known to make whatever you need; not quite a shop, but definitely a place of business, like the village smithy. If that craftsman can make some kind of magic item easily, he may have a couple on hand for impulse purchases; otherwise, he's available for hire.
The important thing to keep in mind is that, even if magic items are easy to make, that doesn't make them mass produced. Compare it to the art world; you usually buy art in a gallery, which has whatever it has, or a studio, where the artist might be available for commission. You can't walk into a random "art shop" and expect to find exactly what you're looking for, and you can't find a "Van Gogh store". You look in a gallery to see if they have anything you want. If, on the other hand, what you want is mass produced, like a Thomas Kincaid, you can find a Thomas Kincaid store. Mass production plus easy to make items will lead to actual magic shops.