How popular is Brazilian Jiu-Jitsu in Japan? Do they like or hate it?

Decently popular but most people in japan have figured out that BJJ is really just Judo with more focus on the Ground. Judo has the same moves and is the same art the only difference is what they focus on. Judo Guys do 50/50 Ground and standing maybe more standing depending on what they are training. BJJ is 80/20 Ground being the 80 20 being the standing(IE the takedowns)

A lot of fighters from Japan practice BJJ, including Genki Sudo (retired), Shinya Aoki, Masakazu Imanari, Daiju Takase, Megumi Fujii, Yuki Nakai (retired), and Hatsu Hioki. Most Japanese MMA fighters, however, have backgrounds in Judo, Catch wrestling, freestyle wrestling, or Shooto, as far as their grappling base. BJJ classes are part of several MMA gym programs over there, but it's still somewhat new.

I suspect, just as in the US and most other places, if they don't follow fighting, the general populace doesn't know what it is.

Idk to be honest if it can be considered "popular" in a country where "jiu jitsu" itself originated. The original jiu jitsu itself can be considered to be popular probably. However, considering that MMA is one of the fastest growing sport in the world, it wouldn't be surprising to see that more bjj schools are opening up in Japan.

Seems to be gaining popularity especially in training alongside Judo or Shooto

its popular