The answer, Witchdoctor, is that people (and by people, I mean all 10 AAAs, GOD, and anyone else that felt the bite of the Shutdown and Crash) have been actively searching for any trace of Deus since the Crash. And they've found nothing. This means there are only a few possible outcomes:
1) The Big 3 AIs died in the crash, and were deleted from the Matrix, though their code survived in the Resonance Realms, since the Endless Archive has a copy of everything that ever was on the Matrix.
2) The Big 3 AIs died in the Crash, and their code was disseminated throughout the Matrix, becoming the 'spark' that started so many AIs emerging. Their original code remains in the Endless Archive
3) The Big 3 AIs 'transcended' to the Resonance Realms, becoming Paragons or other entities within the Realms.
4) The Big 3 AIs (or at least some of them) hid copies of their code in systems that were isolated before Jormungand got to them. However, the computing power required for storing a copy of one of the Big 3 was enormous, meaning you are unlikely to find it outside of corporate or national government mainframes. This is by far the least likely option.
Notice how most of those things have to do with the Realms? You'd have to be a TM (or Otaku) to get to the Realms. And we know (from reading in Stolen Souls and other books) that a Dr. Penelope Anne Xavier (note the initials) was deeply involved in the projects researching CFD, and she says straight out at one point that she has far more tricks up her sleeve in the Matrix than her rivals. And in Lockdown, it pretty blatantly says that Dr. Xavier is not only Pax, but also the one who pulled a fast one, inserting Deus's code into Eliohann's nanites instead of Cerberus's code.