The economics of bookstores in Japan favours the shop owner much more than other places. Books are sold on consignment, you order books and pay the wholesaler once sold. Book doesn't sell, not your problem, return it to wholesaler. Publishers are also allowed to fix pricing on a new book. So you could make money but not a lot as the store owner pays freight.
2006 presentation from member of Japanese Book Publishers Association (English language) https://www.jbpa.or.jp/en/pdf/bookmarket.pdf or more recent from 2022 https://www.jbpa.or.jp/en/pdf/presentaionatTIBE2022.pdf, Both linked from https://www.jbpa.or.jp/en/index.html