Or they already got all the decent personal and equipment, retreated into the shadows, and left Ward with the scrapes.
Well, my question is whether they're Hydra or not.
I think in many ways, that's almost a philosophical question.
Look at it this way: It's a bit like asking if a given terrorist is al-Qaeda or not. By which I mean, al-Qaeda is almost more of a brand name with affiliated franchises than it is a centralized organization -- if some militia gets together, attacks civilians, and declares itself "al-Qaeda-in-Sudan" because they think Osama bin Ladin was the bees knees and they consider themselves loyal to al-Qaeda proper, well, then, that makes them al-Qaeda, doesn't it? Even if they've never met anyone or had any interactions whatsoever with al-Qaeda leadership.
At this point, I think Hydra is like al-Qaeda in that regard. They are Hydra because they think of themselves as Hydra, because they seek to embody that sense of Hydra-ness and are loyal to that conception of Hydra.
This
does reopen the question of just what Hydra's ideology is and what they ultimately want. I think that the conclusions I came to in
this post are valid. They seek not only to usurp the world's governments and rule directly, but they seek also to use science to create a race of fantastical Übermensch who shall reign supreme over the inferior masses: Fantastical fascists who venerate a superior-race-to-come-from-science rather than an existing nation.
Given that... Really, no two Hydra cells need to be in communication with one-another, or aware of one-another's existence, to be equally Hydra. They need only be committed to the idea of Hydra and its own domination of others.
Just from a movie perspective, it would seem odd that after quite clearly saying in the first 15mins of AoU that Strucker's was the last Hydra facility left (and everything in AoS points to his group being the dominant cell) only to have them almost immediately return in Civil War.
But of course, we've been through this before with Hydra, haven't we? At the end of
Captain America: The First Avenger, their bases were stormed, their assets seized, their personnel killed or detained; Hydra was utterly defeated. And yet it sprang forth again, did it not? "Cut off one head, and two more shall take its place."
As a plot device, Hydra has a built-in excuse to grow back from nothing.
Let's add to this the fact that it is not clear that all of Hydra's leaders are dead. We saw Dr. List shot by Tony's repulsor beams in
Avengers: Age of Ultron, but it's not clear that that must necessarily have killed him. He could also have been knocked unconscious, and be held in a NATO prison. (AoU had a line of dialogue saying that the Hydra leaders captured in the opening sequences of AoU were turned over to NATO.)
And of course, we already know what happens when the seemingly unimpressive seconds-in-command of Hydra are imprisoned while the leaders are killed or disappear.