It's campaign and genre dependent for us. In 2 games there are magic item shops. One of those is b/c it's Savage Tides and we don't want to go on detours to get necessary gear, so we just mulch whatever we don't want/can't use. The other is that some magic item creation, purchasing, and trading with people who essentially forage or mine for the stuff (it's a long story, but the short of it is that the world is alive and malevolent, but the flotsam of consciousness leads to it creating all sorts of things).
In another game, though, we really wanted to preserve the feel that magic items are special. Which, I think, is the only argument in favor of no magic item marts. We did this with essentially no change to 3.5 D&D. We just had some items defined as part of the narrative, they "existed," and others were just mechanics stuff on your sheet. This went both ways, too, some of us defined some of our class abilities as the products of other items. It worked fine b/c we were all pretty flexible about it, and what it did is it divorced wealth from power. So, you essentially have two things: gold, that is real in-game money that you use to buy things at inns and castles and stuff, and "treasure points" or "magic item points" that are used to acquire the stuff you need to make your character work.
It's hard to imagine any world with a large number of adventurers without some sort of magic item economy, though. In the Forgotten Realms, for example, there are tons of adventurers and tons of mages and tons of old loot lying around. It defies imagination and verisimillitude that there wouldn't be someone in Waterdeep there to help some poor Fighter who has specialized in the Glaive Guisarme swap the Bastard Sword +3 he's found. This isn't a magic item shoppe, per se, but it's the equivalent. And, unless there's a real reason to role-play out finding someone and trading, it might just be worth it to hand waive it all and treat it like a magic item shoppe. We generally do such things between adventures online with google docs anyway.