I hate 'magic shops'.
Generally, you can go to a craftsman, come back in 1d4 days and pick up something you wanted made.
Or, you can go to a merchantile put down more money and get it immediately. What's generally more important about finding a good merchant is finding one who offers honest prices for the things you want to sell. Generally, I play out the selling portion until such time as they actually settle on a relationship with a merchant, at which point it becomes redundant and I only play it out if there is something unusual in play.
If the town is big enough, it generally has an alchemist who has say 2d8 random potions available for sale, makes about 1 every week as his inventory changes, and will make more on commission up to about 1 a day. Major temples usually have a similar number of potions and scrolls available for sale to people in good standing with the temple. Occasionally, if the town is big enough to support it, there also will be some hedge mage or local wizard who is trying to make a buck and will have a similar inventory of arcane goods. In short, you can often pull quite a few potions and scrolls out of a community in short notice, but generally no magic items more valuable than that.
If the town is big enough to be a city, there will be some guy who deals in spell components, wierd curios, religious articles, archaelogical artifacts, rare maps, art items, and occassionaly magic items. He'll have 1d4 or so random usually minor magic items on hand, some of which he may not completely understand the function of. The guy is often wierd, frequently evil, generally disreputable, and with a clientelle that is downright dangerous.
In the bigger cities, about once a month, a specialized dealer in magic items will come through with about 2-5 magic items and there will be an invitation only auction to sell the items. If the PC's are important enough and rich enough, they'll recieve an invitation. It's a good way to start introducing factions to the players.
In the bigger cities (and occasionally in rural areas where you wouldn't expect it), there are usually major wizards of 6th level or higher who can make moderately powerful items. Generally however, they are quite busy with their own affairs and have no time for random mercenaries. To get in to see these luminaries requires developing a reputation, and then getting them to do something for you requires building a relationship with the person - which generally involves a minor quest. After that, they'll possible accept commissions to make individual items, which are usually ready a couple of days later.
Generally, for me, that's it. I expect the PC's to find most of their magic items, not go shopping for them. I don't really have to prepare lists of items on hand. I assume that if it isn't particularly valuable that its on hand, and that if it is (anything more valuable than an ordinary longsword or a suit of chain mail), then its not. My assumption is that it is a medieval economy, and anything valuable is made to order, not left setting on the shelf waiting for a customer. There isn't enough spare labor or money to waste on making random valuable items in the hopes of finding a customer.