I've been to Japan a lot - Tokyo mostly. But the last time I was there was before I really got into woodworking. And since my business is coffee, I spend a lot of my time there either visiting coffee spots or hanging out with friends.
But, as Michael said, Tokyu Hands is a great place to visit. It's essentially a home goods store with all sorts of interesting stuff. They do have a tool section and that's where I've gotten all of my metric tape measures. It's really great and there are a couple of locations across Tokyo, making it a bit convenient from wherever you are staying. I've recently been shopping at the Ginza location but mainly because I've been staying in the Ginza/Shimbashi area lately.
I do like a place called Kanaya Brush in Asakusa. This is a shop that specializes in brushes. Hand made brushes. Boars brushes. Brushes of all kinds. Brushes you must have that you didn't know you needed until this very moment. Their boars bristle toothbrush is one of my favorites.
If you like kitchen tools and knives, there's another place in Asakusa called Kappabashi Dori (street) that is lined with all sorts of kitchen tools, servicewear and the like. It's my heaven.
The website you shared looks to have some great recommendations. And if you search on YouTube there's some videos from people who go to tool shops there - evidently, the Japanese have a measuring system that predates the western metric and imperial systems. And there are still craftspeople today who will utilize this measuring system over the rest. Fascinating.
And if you search under used power tools japan, there's some massive-looking shop that has all kinds of power tools, used power tools, tools of all sorts. Can't remember the name at the moment but I want to go there next visit.