That is a perfectly fine house rule when running 3e/Pathfinder but it is not the rules as written in the book. By the book in large cities you could find almost any magic item for sale.
1) Basic economics is not a house rule.*
2) Who said the party was in large cities all the time?
3) Just because you are in a large city, it does not mean you know who has what you want to buy.
To return to an example I posted upthread, I play guitar and live in one of the 10 biggest metropolitan areas in the USA. I have over 300 guitar makers (G), a few dozen amp makers (A), and maybe 50 effects pedal makers (P) bookmarked in my iPad. None of those lists is even close to exhaustive.
I can guarantee you that I cannot go into stores here and find any more than 10G, 5A and 12P in any given store. And most overlap their inventories. Sure, se of these companies are small, but many are multinational corporations.
And even so, much of what is out there is only available HERE because of the Internet...even within a brand. Looking at the 2 biggest G brands in the world, Fender and Gibson, perhaps only 33% of the guitar models in each of their production lineups are hanging on a shelf somewhere in this area.
Spinning this back into a campaign world, even in the biggest city of "Fantasy Realm X", no seller's inventory will be complete. And even if he knows someone who DOES have what you want, he may not be interested in telling you where to go to get it.
4) Just because you have the money, doesn't mean you have the legal right to purchase anything you want. Admittedly, this IS a house rule of sorts, but it is one with a strong foundation in the kinds of societies typical of FRPG game worlds. This could result in hugely inflated costs as the party resorts to the black market, or even outright unavailability.
5) Just because it is in a sourcebook, it doesn't mean it exists in the campaign world.
* except, insofar as was pointed out by another enlightened ENWorlder, even gravity is a house rule.