Yes, apparently the organization is the Secret Empire, the symbol is an "A" and the zero matter is dark matter from the darkforce dimension. However, if no evidence suggests otherwise you could always keep as your headcanonlike this:
From ancient times there has been a secret organization interested in power, extraterrestrial/extradimensional artifacts, etc. At some point when the semi-ram skull symbol was the current symbol an offshoot group came into existence that at one point flipped the symbol and made it into an "A", while the main group kept growing, and eventually became Hydra under Johann Schmidt during WWII.
I also think it's funny that after the "ties in to the Doctor Strange universe" comment, everyone, including big news sites, suddenly seem to think that Darkforce is something that has always been associated Doctor Strange and/or that it must appear in the Doctor Strange movie. The first of these things is simply false, and I think the second is very unlikely.