Perhaps it's a bit reductive, but your story reads like "I went to a restaurant I like and they nearly refused service due to my ethnicity".
A similar thing has happened to me and it doesn't make me want to go back.
A similar thing has happened to me and it doesn't make me want to go back.
I sometimes run into that kind of behavior, especially when my first impression is my looks rather than my voice. But then I think of it like this: they probably have to deal with many foreign customers, "most" of whom cannot speak Japanese. Or they might not have been exposed to many foreigners that they know there are foreigners who can speak Japanese.
At the same time, Japanese society puts consideration for others at one of the higher priorities when interacting with people, and is seen everywhere and highly evaluated by many.
So it feels natural for the person to assume that I, as another one of those foreign people, most likely cannot speak Japanese. Also, they could try speaking to me in Japanese, but it'd be inconsiderate of them if I didn't know Japanese. So many a time the default, and very likely considerate route out is broken English to the best of their abilities.
I know this makes people like us who do know the language a bit bad, but then again, we're still a minority so I wouldn't read too much into it. :)
Of course, if the person in question knows you know Japanese, yet keeps talking to you in English, then it might be better to assume something is not right. :)
However it's only happened once in a year of living here and never in Tokyo, only a ruralish city, so I don't take it as an indictment on Japanese people. I'm sure there are plenty of bars in rural America or Australia (where I'm from) that would have been equally unfriendly to someone of Asian ethnicity. At the end of the day you just have to decide not to let it ruin your day that there are some bad eggs in the bunch, no matter which country it is.
*Caveat though that I've heard it is much worse here for people from China than it is for white foreigners such as myself. If it made up a significant portion of my experience it would be hard to live here comfortably.