Steph definitely got screwed by the New 52. Daft thing is, they didn't make it so Oracle never existed - Killing Joke is still canon. As such, Babs becoming Batgirl didn't have to mean Steph giving it up, and if New 52 hadn't happened, it wouldn't have (though Steph would've probably still lost her solo book).
Young Justice is heavily reliant on pre-Flashpoint continuity and most of the Young Justice/Teen Titans continuity is actually restored. Flash Annual #2 actually had Impulse revisit the 2003 Teen Titans team's tower, which was empty. He was looking for Conner, Cassie and Tim, and found them in Young Justice #1. Because the Tower still exists, the pre-Flashpoint YJ and TT are proven to be back in continuity (we also know that at least the Fab Four and New Teen Titans existed). So yeah, all of Cissie's previous history happened. She might have forgotten about Bart's supporting cast though (Max Mercury, Jay Garrick), as they're still missing (trapped in the speed force).