I saw a documentary about the Philippines and Indonesia. Many country people still live in huts and wood houses without windows. This is what houses looked like in Japan before the Westernization. Traditional houses with thatched roofs or just poorly built wooden shelters were the most common habitations in Tokugawa Japan. Nicer merchant or samurai houses were preserved in cities like Kyoto, but all the poor houses were destroyed. Those that we can see in open air museums like the Nihon Minka-en are much nicer than what most ordinary houses must have been.

I think that if we want to have an idea of what peasant houses in Japan looked like at the time of the samurai, and how people lived (this we cannot see in open air museums) the best is to visit remote Austronesian islands. These people are also animists, like most Japanese peasants (Buddhism was for the elites, and Zen specifically for the samurai).