I've been told that many locally owned/operated hotels in Japan don't load inventory until about three months out. They might simply show rack rates far in advance.

For international chain hotels, I'd expect the usual inventory/yield management algorithms to be used, or possibly some minor variation.

Is the OP remembering and comparing prices in yen or dollars or Euro or pounds or.....? Foreign exchange rate fluctuations might explain some of the differences, although again chain hotels might think of rates more in the chain's home currency than in yen, even though most of the hotel's costs would be denominated in yen.

Another factor might be time of year. Late fall is the time to see beautiful leaves in Tokyo, so it's a popular time to travel.