There's a bit more to it. there is a cultural element to this too. And yes, Tokyo as a metro area is about 1/2 the size of Houston for example, with 38 million people. So the density does drive some opportunity. But, the area a couple of those shops are in Akiba/Akihabara (electronics town traditionally) is super interesting. You'll find small shops like that for almost anything and any hobby, and shops like this exist all over Tokyo. For example there is a building next to the metro station that is filled, 3-4 floors, of the small 'stalls' think, about maybe 8x8' size, and each one is a guy sitting there selling 'stuff' mostly in this case small electronic components. Need a resistor, go see this guy, need an IC, go see that guy. They cater to hobbyists and those doing prototyping etc. But you can find anything there related to electronics.
So it's no surprise to me you'll find the same for a tool guy. My other hobbies have the same sort of stores. Jazz records? Go to Hal's in Shinjuku. Need a needle for a cartridge? go to this guy. Love Manga? Go to Nakano Broadway. It's really unique. Love going there every year.