Taking a break from pro. cartography work and some campaign writing to drop more thoughts about this topic into the blog.
Without Magic Shops, where do you buy magic items from?
Herbalists and Alchemists
Herbalists are a good bet for buying a low power potion, especially minor potions which can slow poison, slow disease or heal you for a few points of damage.
Some DM's (like myself), really dig the idea of brewing potions from natural ingredients. I was greatly inspired by the Skyrim video game and wrote up all kinds of plants and herbs which can be combined in various ways to make potions. This sort of thing can greatly flesh out what an herbalist might have for sale.
I think of herbalists as the natural healers in a community. I usually have herbalists double as physicians for the village where they dwell.
Alchemists to my mind are more like crazy scientists, combining strange chemicals with the blood of monsters. If you want a potion that can do crazy things like possibly...maybe...20% chance for sure, turn you invisible, these are the guys you go to. Alchemists are sometimes the guys making poisons to sell in the Underground market.
I would be less inclined to trust what an Alchemist brew to put into my actual body BUT sometimes you need to drink a potion that makes you as strong as a Frost Giant for a few minutes, so what are you gonna do?
When it comes to Herbalists and Alchemists I usually keep them with a very minimal stock on hand plus maybe two or three really wiz bang potions which are the current focus of their experimentation. Herbalists and Alchemists are more likely to brew a potion up "to order" for a customer rather than try to keep a stock on hand.
I also like the idea that potions are always a one and done kind of deal. None of the potions in my world can be broken into individual sips which can be metered out. In my world you've gotta down the whole thing and see what happens. Potions purchased in shops don't always work either. You might purchase a complete dude, in which case most shop keepers will provide you with a 50% return on what you spent, provided you make it back alive to claim it.
There are no smiths, anywhere in the world, who can make you a magical weapon. None. Zip. Zero. Maybe a really talented Dwarven smith could craft you a Dwarven weapon of quality but that will always be a custom, made to order affair taking at least a month to complete and costing in the hundreds to thousands of gold pieces.
There are thousands of individuals living in the fantasy world who would love to get their grubby fingers on a magic weapon, or a magic shield, or magic armor. The demand for these items so totally outstrips their numbers in the world that nobody, nobody is offering to sell them.
Really powerful, high level Clerics and Magic-Users create magical weapons and armor and it can take months and years. Usually when they create these items they are doing it for a very specific purpose - they are not about to make one for some chowder head group of adventurers, no Bill, not even for 10,000 gold pieces.
If, by way of example, a vampire turns out to have a magical +3 scimitar of gore in their treasure trove the vampire is going to be wielding it.
So how do you get magic weapons and armor?
You pry them out of the cold dead hands of their current owners, be that monsters or other types of enemies OR you can sometimes come across one in the horde of an actual dragon. That is about it.
Magic Items and Charges
In my campaign I like magic items which have charges. If there is going to be a flying carpet in my campaign then there probably will only be one. One in the entirety of the world. That flying carpet will probably run off of charges. Sure, there will be a way for a major magic item like this to be recharged. It might require that you place 500 gold piece diamonds on the rug and watch as the run absorbs them for one use to be recharged.
Major magic items usually have a way to recharge them which is both inconvenient and very expensive. More minor items like say a wand of webs, will have a finite number of charges, say six. When the wand is out of charges it crumbles and disintegrates into nothing - the end.
Permanent Enchantments and Magic Items
Sometimes a high level Magic-User or Cleric wants to enchant an area with a certain effect and they want to make the effect permanent. They need to use the spell permanency to do so but in addition, the spell requires the material component of at least a +1 magic item of a value of no less than 1,500 gold pieces. A +1 magic item will grant you a permanent enchantment on a location which lasts for up to 25 years. No forever, but a long time. That +2 cloak of protection will allow you to enchant a location for up to 50 years. Permanent magic items used to create permanent enchantments on Wizard Towers, Temples and Palaces insures that the world stock of permanent magic items is always being drained, at least a little bit.