Given that different versions of the same region already exist with different Dexes, it's just as likely that the new Hisui Pokemon are still around, they're just kinda.....over there, off camera, in the places we didn't go in the other games.Also, here's a depressing thought about Legends Arceus. The Hisui region is the Sinnoh region only a few hundred years in the past, right? I guess that means something happened to make all these new Pokemon extinct by the time DPPt happens. Or Arceus took them all away on a Ark or something by the end of the game. Kind of obvious, but it didn't occur to me until now.
Alternately: we've been able to ressurrect fossils since Gen 1. Extinction is temporary.