Many WiFi spots in Japan require to register or purchase service from the provider. Only in few spots like (many America retails chain) you will find truly free WiFi.
Get get ready foe 2020 Summer Olympics, Japan is trying to crease more WiFi access points ... That is a good news for travelers. Until then, when you travel to Japan, rent a WiFi router at the airport so that you use your own cellular devotes in WiFi mode.