Yeah, not sure where the whole idea of Hydra being completely gone makes any sense. Even within this very show Zemo & Bucky exchange that, the reason why Bucky is enlisting Zemo's help is because he suspects Hydra has something to do with it and Bucky knows that, in light of that, Zemo is their best bet due to his knowledge of Hydra. It's like... The very premise for the coolest character getting out of prison is to stop Hydra and the counter-argument is that a non-cannon B list TV show indicated they were gone.