This is one of the reasons it's important to keep things in context. The DMG does say that anything under the GP limit is "most likely" available on page 137 under the topic of Community Wealth and Population. But the topic on Magic Items on page 142 says that magic items may be available in markets and shops "occasionally".
It's important to consider when the DMG (and other rules) are speaking most generally and when more specific guidelines should apply (specific usually trumps general) and to hold firm when a player pulls a particular statement out of context in an effort to get that oddball magic item.
3e gets a lot of blame for the magic shop issue, but nuts to that. The advice to the DM is there to allow shopping but to make it reasonably low level, uncommon, rare, or significant. The fact that plenty of specific campaigns and DMs haven't followed that advice, and that many DMs have not done so since the days of 1e, is not the fault of 3e in the slightest.
This post gets to the other heart of the matter. I definitely am not trying to convince you that every shop has a +1 thundering kukri.
I wouldn't expect every weapon shop to have every non-magic weapon listed in the PH. I wouldn't expect every magic shop to have every magic item listed beneath a certain value. That belies logic. Even though WalMart is fed by a massive supply chain, they do NOT all see the same stuff. And that's a chain that TRIES to sell all the same stuff.
I am saying that if you play in a world where the PCs have extra items, and they face plenty of foes with items, and there's plenty of NPCs they should not attack in cities that have items, then there is justification for a magic shop. With each shop having a limited selection of items currently available.
It sounds like 4e has some weird guidelines on item availability that contradict what sounds like a low magic, but heroic campaign setting. I think billd91 covers that.