I just came back from there. @kthxbai sent me to some wonderful shops. Nakano train station. West exit. Go straight ahead until you reach Nakano broadway. Mandarake on multiple floors. Second floor is the card shop. I just posted some pics on my collection thread.
It’s actually pretty hard to find a lot of pre XY or later singles in shops. Most shops only carry the current sets, so XY and SM. They cater to players and not collectors as they work on turnover. Mandarake is probably your best option to find older cards.
Also, in Japan stores don’t care about warped cards. You will see tons of $50 SR or UR cards that are really warped. You would figure they could topload one copy and binder the rest of expensive cards since cards warp easily in Japan due to the climate. Also, SM cards seem to warp a lot easier then XY cards.
This is the main shop I go to as I live a 5 minute walk from it xD .
There are some MUCH better shops in Akihabara that haven’t been mentioned yet, but they also don’t have names so not easy to direct. 1 of them specialises in tournament promos and other high priced cards (no rarity holos, fan club, etc). Average card price around 10k-300k yen. But the condition is generally not gem mint, and their prices are more similar to UK market prices rather than y!j. But still fun to look around.
EDIT: If people want, I can gopro around all the shops I know about at some point when I get a chance?
The no rarity Hitmonchan I picked up in a small shop in Akihabara got a PSA 10! No rarity Charizard from Mandarakd Nakano got a 5. There are gems to be found if you search long enough.