Their (very successfu)l head coach had to step down recently due to a harassment scandal. Not sexual harassment (come on, it's Japan) but 'power' harassment (it's actually rather mild sounding;
http://www.asahi.com/ajw/articles/AJ201804070021.html). So that could be having an effect.
On the other hand Takahashi was also beaten in the 1st round so it could be a 'time to peak' thing like you say, they seem to be good at peaking when needed and can have iffy results before that, so we'll see.
Incidentally DPRK won 2 of those women's golds, and the guy who beat Takahashi was also a Nork who went on to win silver, could we be about to see the resurgence of Best Korea as a wrestling power under Kim Jong Un?