It is very easy to rationalize magic shops out of existence in a POL setting, having magic shops doesn't make sense.
OTOH, if you wanted to go for a "realistic" approach, you don't completely eliminate the magic store, you modify it. Otherwise, you're eliminating a chunk of realistic commerce from your fantasy economy.
While many treasures pass directly from person to person, some get lost or sold. People find things and sell them- like the Dead Sea Scrolls. People outgrow their possessions- like a former Cub Scout who upgrades from his organizational blade to a nice Spyderco. How many great guitarists found their first axe in a pawn shop?
The key is that people may not know that what they sell (or buy) is magic.
So, no "One Stop Magic Shop"- what to replace it with?
Much like the real world, minor things such as potions should be available in such a store- be it an apothecary, alchemist's, or the dwelling of a hedge wizard at the edge of town. Depending upon the local social climate, visiting such a place might be risky...after all, who wants to be associated with a witch who consorts with
demons?
Other items would be found among mundane items of their kind. A magic sword would be found at a weaponsmith's. If he knows its magic, he'll charge for it. If he
doesn't know its magic, probably none of his customers do either. Of course, without the right skills or spells, neither will the PCs. Selling/buying a magic weapon (unknowingly) is even more likely if local laws restrict the right to bear arms to a select few. Holding onto a sword without the right to bear one would be foolish- better to sell it off for a few gold and eat for a fortnight. (On a certain level, this turns shopping in town into a treasure hunt in and of itself.)
Still other items should be in the hands of private collectors, armories, guilds, churches or schools. Access to those- either by loan or purchase- would be granted via connections made in game, PrCls, or perhaps an adventure like a raid on a merchant's summer house...
And, of course, this keeps open the possibility of a plotline involving the PCs getting defrauded by a dishonest seller, or finding out that the Church's relic that they were entrusted to use was just a "wallhanger." (Again, with RW analogs- how many young men have died because a shaman told them they were protected by magic that simply didn't work?)