Just to let you know Nintendo is not a Japanese company. It's a Kyoto based company. Their structure is vastly different from others in Japan, let alone the world. From a business point of view they are doing things that fans won't understand and fans don't need to.
I'm confused by your first two-sentences, as Kyoto is in Japan, unless we're only counting the Tokyo region as culturally/economically importatnt to Japan. Kyoto is a big city too, though, so it's not as if it's a world of difference from Tokyo.
In regards to the OP, I don't entirely know what the rationale is for the New 2DS XL, but I guess they saw a market for it. The NES Classic I can understand as to why they discontinued it, because it was mainly support to be a console to fill the gap between the holidays and the Switch. The supply issues on the other hand, I do not understand why they had that problem. Nintendo are obviously in a very safe spot financially, so they they're probably not doing too much to dissatisfy their shareholders.