So, my two ¥ worth here, but I haven't seen this posted yet so here goes.
I think Deus is still out there, and we will see the return of the Big Three AIs(in some form or other), for another couple of reasons entirely; Nostalgia and Paranoia.
To explain, Shadowrun has always been a universe where a healthy amount of paranoia is a good thing. There ARE dark things lurking in the shadows that we barely understand, and they ARE dangerous if you don't watch your back. That spine - tingling, nerve-twitching, Oh Drew What Have We Done Now feeling is integral to the atmosphere of the game, and it's been heavily involved with the most popular modules to date.
Ask most Shadowrun veterans what they're favourite published settings and adventures are, and you hear the same two come up again and again - The Universal Brotherhood/Bug City, and Renraku Arcology Shutdown/Brainscan(also System Failure, but to a lesser extent). Both of those story arcs thrived on deadly, unfathomable foes that were nigh - impossible to understand, deadly environments and a fight for survival, and not knowing who you could trust. As much as Bug Spirits and Medusa drones probably ammounted to more dead PCs than all other enemies combined, players loved them and the adventures they came from.
Which brings me to the second (technically former) point. Nostalgia.
I think Catalyst has realized that they want to recapture some of the original cyberpunk feeling of the early editions while still moving forward and advancing the universe and story lines they have, and so they're taking a cue from their most popular story arcs. Now, they can't simply redo Bug City over again exactly the same, but in 4th edition we've already seen some major information drops and hints that the Bugs are more insidious than ever, and may have infiltrated some pretty high levels of ARES. So while the bugs aren't back per-say (they never left), they ARE still out there and dangerous and possibly better positioned than they were before under the guise of the Universal Brotherhood.
So now with 5th edition and the CFD virus, we're seeing the technological side of paranoid again, where nanites are taking people over and people are scared of the technology that they thought themselves the masters of. Plus we know that PAX is back (pretty much confirmed as Penelope Anne Xavier without actually coming out and saying it), and she was obviously one of the main NPCs of the Arcology/Crash 2.0 arc.
Now, I don't think they'll be back in the same way they were before, but in another form they will be. Perhaps as powers behind the scenes pulling strings, perhaps as new options for Resonance or Dissonance paragons (it was suggested in a 4E book that Morgan was Dodger's personal paragon, though that was just sentiment and speculation by Netcat at the time), I really don't know. But I am pretty darn sure they'll be back in some way. Because as far as Big Bad Scary Things go, Deus was one of the worst (or best).