I just think having magic shops with hundreds of items available, each costing a small fortune, is implausible and senseless.
It's all about inventory and volume.
If in your campaign, there are ZERO magic items, then there will be ZERO magic shops
If in your campaign , there are FIVE magic items, there still won't be any magic shops, and odds are good nobody's buying or selling (prolly killing for).
However, if you play in a world where NPCS clerics and NPC wizards are cranking out minor magic items (potions and scrolls), you have the foundation of justification of a magic shop.
Note, I define magic shop as a place that sells magic items, not services. It's also entirely plausible that you can only buy magic weapons from an arms merchant. The nature of the shop is unimportant, only that there is an NPC that PCs can go to, and buy some magic items.
When you consider how many extra items the typical PC gets by 5th level, 10th level, etc, you start getting into having a SUPPLY of magic items.
From there, obviously the PCs want different magic items or money (so they can get different magicitems). This is the DEMAND.
Consider the old rule of thumb that 10% of the population is leveled (i.e. NPC adventurers, etc with level appropriate loot). This means that in a large enough population, there are NPCs with similar piles of unwanted magic loot. Once again, creating supply and demand.
At that point, some enterprising individual (likely an NPC adventurer looking to convert his unwanted magic items) will start a business selling and trading items. And making money off it.
All it takes to justify this is two categories of people:
1) minor item makers who crank out commodity items like potions and scrolls selling to adventurers (PC or NPC)
2) higher level chars with items they don't use, looking to trade them in for stuff they can
Given how easy it is to crank out the small stuff, that justifies a "magic shop" that sells the small stuff.
And if I was a new PC, I'd be looking there for magic stuff in general, because those folks are in the know.
And if the campaign I played in was fairly generous with items, I'd easily have stuff I don't want (yay, I found a +2 sword, maybe I can trade in my +1 for something else).
Businesses exist because of SUPPLY and DEMAND. There is DEMAND for magic items, it is the number one reason PCs go adventuring for (that and XP and gold). The SUPPLY is the total magic items in the world. They are not all sitting in a dungeon, waiting for a PC to find it.
There is a demand for a whole lot of things in our real world. And there are people making businesses out of it. Just because you don't like the idea, doesn't make it unrealistic or unfathomable. Otherwise there wouldn't be the gambling, drug trade or human slavery. If people want it, somebody will find a way to get an inventory and sell it.
I suspect that the real root of not wanting magic shops in a campaign has more to do with GM control. The extreme example of anti-magic shoppism is that a PC can declare what he wants and walk into any magic shop and buy it. These types of GMs seem to loathe the idea of a player getting whats he wants. Whereas, all the examples by GMs who accept the idea of magic shops point out that the DM has full conrol of the inventory and prices. Many of these examples include some rather clever integrations with other real world business ideas. I've not seen one example of a magic-walmart, where a PC can buy whatever they want and run rampant over the campaign.
In short, barring a low magic campaign where there isn't enough excess magic items to sell, it defies logic and real world comparison that there would NOT be some form of magic shop.