There are four card shops in Nagoya proper, a pretty good number for an often-forgotten city that happens to be the fourth largest metropolitan area in Japan. The Tokyo area has over a dozen (possibly nearly 20) shops but four seems to be about the max for the other regions.
Earlier this month, I spent my weekend in Nagoya and had a pretty good time running from small amusement park to small amusement park, and visiting a couple tourist attractions in the area. I made sure I had card stores on my itinerary and I managed to go to two of the four - one was closed for a short summer vacation and the other wasn't reachable in the time I had.
I've been to Mint Ponyland before, but I guess I need to change my opinion when I said it's the best store for singles. It is true that they have a ton of singles of mainstream BBM, Calbee, and the recent third-party releases (Frontier/Epoch/a couple of the CCGs) but I have yet to find a lot of true oddballs.
Mint Ponyland is more than adequate when it comes to picking up singles from regular releases. I'd say it's the most organized card store I've seen in Japan and it has plenty of pleasant surprises. But I didn't see any old Calbees, insert cards, or a really good selection of autographs from NPB products. They could be hidden, and I am going to return sometime anyway!