You could ask the same thing of Wizards of the Coast who sent goons to a guy's house over some Magic The Gathering cards.

We live in an age where these two things are becoming interchangeable.

In 1999, Nintendo got a woman in Japan arrested over - and get this - sharing erotic fan art. I've read they also might've sent private detectives to stalk after her before the arrest, but couldn't find anything quickly. Anyway it sparked a big shit storm and a debate about what copyright holders are allowed to do, legally and morally.

It's not even the first time they've done this shit

I read an article about a leather artist who recycled secondhand Gucci (I think? It was a big name fashion brand is all I recall) bags into wallets and things like that, and despite everything being clearly labeled to make sure nobody could mistake it for an official product, they had a similar experience. I wish I could find the article again, because I don’t remember what came of it and my search skills are failing me.

Yes.

They are from Japan, so yakuza? They probably just hire local muscle, though.

I mean, they are located in Japan, so it's not like Yakuza don't exist (though to be fair Yakuza don't really target foreigners).