You see quite a lot of Indians / South Asians in cities like Tokyo and Kobe. Elsewhere in Jpn... not so much. However, interestingly there're Indian-run Indian restaurants all over Jpn, even in cities on the countryside. Jpn's becoming increasingly multicultural. For what it's worth, one of my best friends is Indian-American, and he had a great time in Jpn. Of course, there're stupid ignorant people everywhere. Unfortunately, Jpn's got some of that, too. But odds are, your friend will be just fine and I'm sure he'll enjoy Jpn.
On a related topic, by the way, how do you go about wandering in various restaurant/bar districts and finding interesting and affordable izakaya to visit and eat in, for example?
I often look at Tabelog, which is a restaurant review/ranking site. So with independent places, it's either word of mouth or do research beforehand. Without that, I too would probably gravitate towards chain izakaya places (I'm Japanese). Chains like Watami are pretty reliable and always enjoyable. I've been burned before by independent izakaya places that looked good from outside... mediocre food, otoshi that you can't even turn down.