In shops and department stores, I have never had a problem in communicating with the clerks. I just generally point to what I want (I find out first if the clerk or someone else there can understand English) and the prices are generally plainly marked.

In other places, I usually have no problem finding an English-speaking Japanese person. A lot of Japanese that I've encountered have a decent, rudimentary command of English. Generally, I have not found the communication problem that a few are sensitive about.

I look at it this way, when I am in Japan, I am a guest in their country. I find it a little odd that foreigners who know Japanese, who are also guests, should get upset if they are asked if they speak Japanese. Since I don't know Japanese, maybe I am not a good person to ask.