:Breaking it down point-by-point: 
 ::1. Yeah, we know Roark is dead. We didn't need Stephen's papers for that, so these are irrelevant. 
 ::2. As you said, we already know this so not really important. 
 ::3. As of right now, we don't know if Hydra is a Who or a What. Keep in mind we have SEVERAL references to Greek Mythology and astronomy (Ares, Orion, Perseus, Corvus, etc.) While I'm of the opinion the pattern IS significant, we don't have enough information yet to determine just what that significance is. IIRC, the only codename given for the Intersect Project itself has been Sandwall, (Chuck Versus the Nemesis) and the only mythological/astronomical references in regards to it has been the codenames of Stephen and Busgang. They could just be members of a government think tank who happened to be working on the Intersect as well, rather than the use of those names being directly connected to the project. 
 ::4. They're captured. Good to know, but probably insignificant. I'm sure this is just going to end up being background on Stephen's private spy activities and irrelevant to the plot of Season 4. 
 ::5. I disagree that we can automatically conclude Mama B "went missing" rather than leaving. She may still have left the family by her own decision like Stephen did later, and only vanished sometime after (for all we know, she was still in contact with Stephen after she left). This is the only point that we really have ANY sort of substantial information on, as the episode seems to imply Mama B is under protective custody. But even that's not enough to really draw any conclusions. 
 ::6. With the Fornax Group we only have a name, nothing to specifically connect it with the unidentified threat Stephen mentioned. It may never even appear in Season 4. 
 :There's just not enough to "gather" or conclude anything.