|Taken from Google, not a photo from one of my local stores|
My experience with these places is generally pretty good. Unlike my experience buying modern used games in the UK, everything in Japan seems to be in pretty good condition and I've yet to purchase a game that just flat out didn't work. However, while you won't really have any technical issues with Japanese retro games, you do have to be careful not to get completely ripped off.
You see, when it comes to Retro games there are two kinds of shop. There's the general purpose shop that happens to have used retro games (E.g. Book Off) and the specialist stores that focus on stocking everything retro.
Specialist shops are usually way better in terms of selection and quality but you really have to be careful in these places not to get completely ripped off. They tend to have the more uncommon games but for a hiked up price and I can't really see the real reason as to WHY the price is so hiked up.
A really good example of this is Megaman 2 on NES. I would see that quite often in the specialist stores for about 1500-2000 Yen (let's call that around $20). However, one day while browsing the aisles at my local Book Off I found a Megaman 2 cart for 250! Yen. It works perfectly and there isn't any damage to the cart so I don't know where the other stores are getting their goddamn prices from.
That's not to say that all the specialist shops are terrible though. A place nearly me will sell you any 3 retro games for 1000 yen as long as individually they cost less than 800. It's a damn good deal and I've increased my Super Nintendo collection pretty dramatically thanks to that place so really it's just a case of picking and choosing.
I think the real key to amassing a decent retro collection is patience, especially if you're like me and constantly on a budget. Sure, you could splash out for that game and get it RIGHT NOW or just cross your fingers and hope it appears inside a Book Off one day for about 500 yen.
No matter where you go though, Japan is easily the best place I've been in terms of choice and quality for retro game shopping.