All the Big 10 have scoured the Matrix looking for any sign of Deus or Megaera, at least, and no signs have been found. That does not mean they aren't out there, somewhere, just that they've been too good to get caught. As for what happened to them? It is possible they were destroyed by Jormungand. Or they could have escaped into isolated systems, and since hidden their trail (such as 'rebranding' themselves as other AIs). Or they could have somehow 'transcended' to the Resonance Realms. Dodger is STILL looking for Megaera, though there seems to be some evidence that he has become a Technomancer, and Megaera is his Paragon. The true answers are probably hidden somewhere in the Resonance Realms, such as the Endless Archive, where everything that ever was in the Matrix is stored.