Well there must be some element that was leaked to the general public, why would there be the AI/Technomancer scare that occurred during 2070 and the Emergence? Not like people in the Shadowrun Universe seem to take kindly to things that are different from plain vanilla human (Metas, SURGEd, etc.), but unless there was some previous reason to be afraid of AI/Technomancers then why would the public react the way it did in Emergence?
Because the news about Deus was released long after they'd resecured the Arcology and long after the newest story had taken over the attention spans of the public. Once they started liberating large amounts of people who had been there for months or longer, it's hard to sell Joe Wageslave on ecoterrorists when everyone they pull out is screaming evil AI.
Stuff that's just taken for granted as universal (not a pun) knowledge in the shadows is completely unknown by average people. Everyone and their brother knows that Universal Brotherhood was a massive megahive of insect spirits, right? Well, maybe in the shadows. But Joe and Jane Wageslave still buy the official story that it was tax problems. Yes, even after Chicago (which they didn't know that was insect spirits until long after the containment zone went up).
I'm again going to edge in on political flamebait, but I'm not saying my position is on one side or the other of this issue...only using it as a real-life example. After September 11, 2001, conspiracy theories started popping up that it was an "inside job". They came out with a lot of scientific evidence, but got very little mainstream media attention. After a few years, the facts started slowly leaking out. Now a large percentage of the American population now believes that the US government engineered the attacks on September 11th. Another large percentage still buy the official story and believe that the other side is full of crazy conspiracy theorists.
This is most likely how things like the Universal Brotherhood, Arcology shutdown, truth behind Tir Tairngire, cause of the Crash 2.0, Damien Knight being a member of Echo Mirage, etc. goes around in the public eye of the Shadowrun world. Most people buy the official story, a few people know the truth and try to get it out, eventually some people find out the truth and some people believe the official story.
Again, I'm using real-world situations as examples. I do have opinions on all of these issues, but I'm not going to talk about them in this environment and hope others won't either. I'm just using these as examples of how the situations we have already experienced in the real world mirror what has happened in Shadowrun.