I had a similar experience with my Civil War build up re-watch, with both Avengers and Captain America: The First Avenger. Obviously, The Red Skull knew of alien artifacts and probably about Inhumans, but I don't believe that he believed that Hive still lived or was recoverable. He believed in Hydra's goals, but believed them to be achievable only through science, not in archaic rituals and human sacrifice. In my head canon, in his megalomania, the Skull believed that by taking Erskine's serum (which he believed to be the equivalent of terrigenesis), he would supplant Hive in the mythology and become the Hydra god that ruled the world himself.
That's a good point, Col. Philips did mention they worshiped Shimdt like a god, maybe that was part of the indoctrination kicking in.
And I'm sure Hydra members have various reasons for being involved, I doubt that Garret was ever a true believer, either.