Suica has been working fine for me in every single bus, train and subway I've taken within Tokyo, and is also working fine in Osaka as well, so I don't think there's anything to worry about for the most part.
Again, Super Potato is overrated. Go to Mandarake or any other of the million retro shops. Also, don't jump on the first Famicom carts you find. They are literally everywhere, even in department stores like Tsutaya.
Just a note, I haven't been there yet (in 2 weeks!) but I'm fairly sure the Evangelion store in Ikebukuro is the only one now - the store in Harajuku closed in 2014 or thereabouts.
I'm mainly going to Super Potato just to have gone, I'm aware they're pretty much picked clean nowadays. Not much of a retro collector so it's more for browsing/gawking.