IMO, Magic tends to be common enough that some sort of shop for Magic certainly has to exist. Now, it wouldn't be anything like Walmart though where you could browse aisles of Magic Items. I think there would probably be two versions of the shop.
1. A Wizard setting up a little area and when the PCs buy an item, they are paying the Wizard to start making the item and in 1day/1,000gp, the Wizard will have the item ready for them. However, the PCs, as part of the price, will need to pay for any necessary scrolls [or perhaps part of the repeat option, he offers to buy the scrolls himself; depends on how well they know each other].
2. A person has a shop, but all of the items within the store are replicas except perhaps the potions and a number of items worth like 1,000gp or less. The rest of the items are stored in a secret, highly protective place.
I also figure there would be some sort of black market area for magic items. You know, like talking to a cloaked figured in an alley. Maybe you'll get what you asked for, maybe you won't. A lot more items can be found this way, but the risk is also much higher.
That's my personal preference of how I think Magic Item 'Shops' would work in dnd while keeping in with the spirit of dnd. I mean seriously, in the real life, if you know the right people, you can buy pretty much anything. I think dnd should be the same, which also keeps some realism, IMO.