In the 2e Waterdeep boxed set, there was a single magic item store listed, and that was a wizard guild selling a very small selection of items not particularly useful for adventuring, as well as a selection of scrolls, and only selling them to members. Other than that I couldn't find any magic item shop listed in City of Splendors. In 3e, the sale of magic items across the Realms became more common - OOC because the game supported it, IC because the Red Wizards started moving into places and selling items.
I just looked in the 2e City of Greyhawk boxed set, the only "magical item store" listed is the Guild of Wizardry, which is listed with the following information about selling items:
The DM is advised to be very careful about selling magic items. Minor items such as potions of healing and the like, and scrolls of spells of level 1-3, are fairly readily available. Permanent items are rarely sold, almost always being retained for use in bartering for items the Guild of Wizardry wants for itself.
It also notes that GMs should set the prices in accordance with other prices in their campaign and that the XP values for items are not prices, just indications of relative values. The PC's items are considered to be valued at 75% of the standard price (85% for guild members), and if the party wants to buy items outright instead of bartering other magic items in exchange, the prices are 115% of the standard price (110% for guild members), and elves suffer a 5% penalty on both buying and selling because the mage responsible for the transactions dislikes elves. The Guild also accepts commissions for the creation of custom magic items, but it takes a while and is not cheap.
There are also pretty strong admonitions about using magic within the city, particularly anything that could cause damage (
Fireball can result in arson charges), violate the integrity of other persons like
ESP or
Know Alignment, or spells that can be used for nefarious means like
Invisibility. And this is in the central city in the campaign setting, being both one of the largest (if not the largest) population centers and the trade hub for the continent. I think Greyhawk in 3e was a little more free with item purchases, but as you said about 3e FR, I think this was more because the system supported it, not because it was appropriate to the setting.
Now for a setting like Eberron, I can see magical item stores being much more ingrained to the setting, given how magic in general is much more ingrained into day to day life in Eberron.