On eBay there's a seller based in Nagoya, they have an eBay store but I don't know about a physical one. Do a search for PC-FX (which is what I was poking around for) and you should find them.
That being said, any game seller that carries used PS2 will carry used PS1. That includes the normal big boys like Yamagiwa, Sofmap, etc. I don't know about Sofmap Nagoya, but if they are anything like Sofmap Tokyo or Sofmap Osaka the main stores that carry console games will carry older stuff -- usually FC, SFC, Saturn, PS, DC, etc.
Although I was in Sofmap Namba today (in Osaka) and they seemed to be clearing out alot of their older stock. Supplies may be limited....
I haven't been to Mandarake Nagoya -- even though their shops are generally anime related, not game related, they tend to carry some good stock. Both the stores in Osaka carry some nice stuff, and the Mandarake Galaxy store in Nakano (Tokyo) was R10 land last time I was there (they had a Darius Alpha, an Eyeful Home, and a Heim Waltz. Obscene.) They'd be worth a check, and there's a map to them in English on their
website.
I plan on giving a thorough inspection of the Nagoya retro scene in a few week, though
