Seems so. Either both Kanda and Yamano failed to meet their sales quotas or FMIC bought out the contracts. I'd guess it was the latter, but who knows.
No evidence any factories will close since there wasn't a Fender Japan factory. Instruments were made to spec by different factories over the years. Those factories will probably go on making whatever other brand instruments they made. And maybe some of them will still be Japanese Fenders, e.g. the Geddy Lee Signature, unless they plan on moving its production to another country. Hope not.
The Japan exclusives are now gone from the website. The offerings are pretty much the same as in the US.