Hydra motto is ""if a head is cut off, two more will take its place"
so can never wipe them out totally one
I guess the idea of Hydra isn't really as an organisation after the real Hydra is gone, but as a methodology and an idea. Like how ISIS is more like an Idea now than an actual organisation, and even Nazi, which is considered a party/organisation, but after ww2, it became an ideology a symbol of racism, violence and death.
Probably also why Hydra is frequently used as the "Scapegoat" in a lot of the bad things that happened in the Marvel movies. Anyone can use the Hydra name to do what they want, if you kill that person proclaiming to be Hydra, someone will eventually do something that's like what he did.
