I think it would help a lot if you were significantly more specific in your questions (I think I see 3 questions in your post). Japanese history spans thousands of years. What particular era(s)/time period(s) are you interested in? Japan is also very diverse geographically and socio-culturally. Ethnographies tend to be fairly specific beasts insofar as they (usually) examine a particular set of people living in a particular place at a particular point (or period) in time. For instance, Dorinne Kondo's Crafting Selves: Power, Gender, and Discourses of Identity in a Japanese Workplace offers a very interesting and thorough look at a group of Tokyo factory workers in the 1970s and 1980s. So, if you're going to set part of your novel in a 1970s or 1980s Tokyo factory, it would be very useful, but if you aren't, then it probably won't be. Somewhat more broadly, Tessa Morris-Suzuki's Re-Inventing Japan offers a fairly broad-based look at Japanese history and culture, but it does presume some background knowledge and is probably somewhat outdated at this point.

I don't really know enough about the hidden villages to answer your question about that.