While the MCU movies haven’t touched on Japanese organized crime, Daredevil explored the Yakuza in its first season, as the leader of its Hell’s Kitchen operatives, Nobu, was allied with Wilson Fisk, a.k.a.
Once The Hand and its supernatural roots were unveiled (they returned in Daredevil Season 2 and Iron Fist), the Yakuza cover was no longer necessary, but that was just one branch.
How exactly Avengers 4’s Japanese gangsters will be used is unclear, though it’s likely that they’re just a minor nuisance that some of the movie’s superheroes have to deal with rather than being goons for whoever the main villain ends up being.