I agree with you. Many Jedi weren't shown in Ep. III, doesn't mean they're dead. I have two explanations on why she's not in Ep. III:
1. She and Anakin have a huge fight and he ends up hating her. (Sad, she's a really nice girl, and Anakin and her make such a good team).
2. She becomes Sith. (Unlikely, Dooku has a bunch of Dark Acolytes already, and Ventress is practically Sith now.)
Oh, and all those who think Anakin has to turn bad in the show. In Attack, his mother died, so of course he was acting all angry. In III, he's worried about Padme. As evidenced by Phantom Menace, he's not evil all the time. Maybe these are his good times. Plus, the show is aimed at a slightly younger audience, no way he's going to go that emo fast, or at all (in the show, that is).