Barry was familiar with all of the Justice Society by sight and knew their secret identities(huge comics nerd that he was), I don't know if less notable characters had comic book versions on Earth-One. And this does bring up the Fridge Logic question, "wouldn't then Barry have known who Batman and Superman are under their masks, as well as any other kid who read comics back in the Forties?" So evidently Earth-One didn't have comics about the Earth-Two Supes and Bats.
The "appeared in comic books" thing was mostly or completely ignored when Black Canary came over to Earth-One, because it would have blown her Secret ID out of the water.