The Japanese usually focus on a team or manufacturer rather than the drivers themselves, so I’m not sure if Honda or anyone else would make that investment. If a Japanese driver were to be successful that could change but, Kobayashi aside, there’s no-one who stands out coming through. It creates a bit of a vicious circle.
I think much of the problem is that most of the best drivers stay in Japan and eventually get into FN or SuperGT (which can eventually get you into Le Mans), when neither of these series get much attention from the European teams that matter. Nakajima, Kobayashi and Sato all came to Europe, but for various reasons they’re very much in the minority.
Even when FN was well regarded, most of the drivers who went to F1 from there were foreign (Ralf, Frentzen, De La Rosa, Salo, Irvine).