My Indian acquaintances (inclusive of close friends and family) who've lived or visited Japan have been generally as positive about the place as my European-American acquaintances have been. I'm talking about the experiences of people who went to school in Japan, went their for work as C-level execs or entry-level professionals for US MNCs's Japanese subsidiaries, were sent there on military orders, tourists, etc. The Japan of the 2010s is a more open place than it was in say the 1980s and 1990s.
Tourists of ethnic Indian origins doing tourist things there will more or less encounter the exact same thing other foreign tourists experience there. I wish the same thing could be said for other parts of the world.