Japan nowadays is not book early is cheap, can be more expensive too as many people think this way so those early, the hotel put higher rates.
When nearly to date of stay and the hotel still did not managed to sell enough rooms, this is when they slash rate.
Go check again when nearer to your stay, you maybe surprise can get similar accomodations at cheaper prices.
I do this frequently, book on agoda first, then nearer to departure, look again, when find cheaper good deal, I cancel the original booking replace with this new one