As other comments pointed, this caste system itself isn't really a "secret". We learn in school that it had existed, and there are quite a few stories dealing

As other comments pointed, this caste system itself isn't really a "secret". We learn in school that it had existed, and there are quite a few stories dealing with it (A novel "The Broken Commandment" (破戒) by Touson Shimazaki, and an epic manga series "Kamui" (カムイ伝) are among the best ones; both have been translated to English). However, things got complicated in modern society; officially the government denies the discrimination exist; some people still keeps prejudice; and the topic is used as a political tool.