That entirely depends on the economy of the campaign. I don't picture there being such an economy in Middle Earth, for example (perhaps there was, but it's not how I picture it). If magic items are expensive/rare enough that only rulers can afford them (and, for example, adventurers, if very lucky, might find long-lost swords belonging to long-dead kings), then where's the scope for a black market. To go back to one of your example, if MTG cards cost hundreds of thousands of pounds each, then there wouldn't be FLGS with cases full of them. Of course, most D&D campaigns do have magic items much more common than this, but it isn't a given.
There don't have to be "cases of them" though. There only has to be one - the one the PC wants to buy. Anything else is pretty much immaterial. There was a trade in artefacts in the real world throughout the Middle Ages and art has been traded and dealt in for at least that long and probably much longer. All this despite the fact that both artefacts and art were far out of the reach of the vast majority of people.
If you don't want magic shops, that's fine. It's your game world, do what you want. But, I'm not really buying the justification here. Magic items are permanent, meaning that even if only one magic item per year is created in all of England (to pick a geographical location), by the time of the Middle Ages, you have a thousand permanent magic items floating around. More if you think that pre-Roman societies could also create magic items. That's more than enough to have an economy.
The issue, from a world building standpoint, is really that PC's often have FAR too much wealth. It's ridiculous that by about 7th level, a PC (and certainly a PC party) is wealthier than some kingdoms. At least in terms of buying power. They've got buckets of treasure. And the reason they have buckets of treasure is because adventures are designed to give out buckets of treasure. Why on earth would an orc tribe have a gem worth a thousand gp? Imagine if I said that every hamlet of 30-50 humans had several thousand gp worth of easily portable wealth. It would be ridiculous. Yet, adventure after adventure, those kobolds or orcs or trolls or whatever, are packing around thousands and thousands of GP worth of treasure.
Why aren't humans constantly raiding orcs? Orcs are pretty obviously richer than humans.