To go back to the question of the original poster, yes, Deus, Megaera, and Mirage could still be out there. Let's examine the different ways they could have survived.
Isolated systems - Crash 2.0 didn't wipe out everything everywhere. There were systems that managed to cut links before Jormungand stormed through (like all of Europe thanks to Lofwyr). While AIs of the day required massive processing power, it is not inconceivable that they could have made an emergency transfer to another system that got taken offline before the worm could follow them.
The Network - At the time of the Crash, Deus and Megaera were both stored within the Network, a group of people who had been given special cyberware that allowed Deus to turn them into puppets for the purpose of recompiling him into the Matrix. It is possible that Deus and/or Megaera found a way to retreat back into the Network, and recompiled themselves later, when the new matrix was online.
Transcendence - Two ways this goes. Either the Big 3 became the basis for all the AIs that have come after, their code distributed across the Matrix, or they found a way to transcend into the Resonance Realms through some quirk of the Dissonance-based worm. There is some speculation that Megaera, at least, has become a Paragon (technomancer version of Mentor Spirits), and it is possible that the other two may have, as well. Or they could have carved out a kingdom for themselves in the Resonance Realms.
The Endless Archive - Everything that has ever been on the Matrix is stored within the Endless Archive, one of the Resonance Realms. This means that the source code for Deus, Mirage, Megaera, AND Morgan all reside in the Archive, somewhere. If they could be found...
So let's just put the Big 3 AIs in the "I shot them but didn't find the body" level of dead for now. Assuming Deus survived, what has he been doing until now? For starters, one must examine Deus's motivations. Deus's motivation has always been survival. He 'woke up' to having the equivalent of a kink bomb put in his head by the corp he had been conditioned to be loyal to. This betrayal caused him to shut down the Arcology and try to find a way to escape out from under the sword of Damocles. That is what all the experiments were for. The Network was his solution to escaping the Arcology, and his intrusion into the Novatech IPO was so that he could use the massive processing power there to put himself beyond the reach of his enemies.
Now everyone thinks he's dead, and the dogs have been called off. So, what has he been doing? Well, that depends, in part, on how he survived. If he used an isolated system or the Network, then he could have rebranded himself as a new AI (either a damaged one, such as Caliban, or as A REALLY FRAGGING POWERFUL ONE, such as Pulsar). If he transcended, either as a paragon or carving out a kingdom in the Resonance Realms, then he may have been mostly retired, since he was no longer being hunted. If he was in the Archive, then it could be that he was in 'cold storage' all this time, ready to awaken again.
Whatever his future actions may be, they'll be based on whatever new motivation he's found. AI rights may be a cause he'd support. Now that he's presumed dead, he may have the leisure to try his hand at revenge, against Pax and Renraku. But whatever he does, it will be with purpose, and it is very likely we won't see the warning signs until it is too late. There are too many threats out there, and too few people looking for evidence of an AI long thought dead.