Or may be they're just vanished / not coming back during a mission so they were presumed dead?
But somehow, that kind of story gave me Spider-Man's vibes.
Well, for my take on a Sega Cinematic Universe Shinobi movie, I like the idea of the Oboro Clan being descendants of noh performers turned ninja and the Zeed using the entertainment industry as a form of espionage.
I like the concept of Joe being half-Japanese, half-American. The idea that while he works hard to be a great ninja, he never feels he quite belongs with his own clan.
As for Joe's cinematic origin story let alone Shinobi movie adaption I don't know.