Last time I went to Japan, I did not see any signs saying "Japanese only" at all. But I am very concerned about discrimination against foreigners there, because there are foreigners who DO know at least a fair a level of Japanese, who ARE aware of bathing etiquette etc., who love Japan, and want to integrate within the Japanese culture, who want to go to/dine/party etc. at places where the local Japanese go to. This includes the onsen. While I can understand why there are separate onsen for Japanese and foreigners, I am personally against that, because tourists with the attitude above want to bathe in the same onsen as the Japanese.
There is a naturalised Japanese citizen of American descent called Arudou Debito, who compaigns for foreigner's rights in Japan. Try Googling his name, or looking it up in Wikipedia.
Debito Arudou - Wikipedia, the free encyclopedia