Regarding Deus: No, he didn't have control over a large portion of the Matrix moments before Crash 2.0. He was still inside the ECSE servers along with Megaera and Mirage, even if there were major processing connection increases from opening tunnels to other matrix sites, when Puck (that frickin' idiot) dropped a Jormungandr code egg at their feet and shredded them to microbytes.
Next, you/we/they/SR has not recognized what's been going on until the De La Mar Matrix (hereafter DLM2) rolled out. If you take a close look at it, it isn't all that much of a redesign; it's more along the nature of a tightening of certain security protocols, a very minor adjustment of the interface protocols, and a revamp of how the networks interact with each other. The baseline coding itself hasn't substantially changed from 2.0 to 2.1; there wasn't a third UMS conference like there was for the original Matrix, in Tokyo in 2039, or for Matrix 2.0 in the Silicon Glen conference in 2065. Step back from 'how rolling the dice in the game' works for a bit, and take a look at the functional changes, and you'll see that that's right.
Truth is, I think they became aware of 'the Foundation' via Dodger's search for Morgan/Megaera. Remember first that he'd worked for pretty much all the major computer organizations - the Big 10, bunches of the smallers, IIRC - analyzing their code, etc. Second, he was a consultant on the DLM2, which means they were in position to reap the benefit of his research. It's like air, or gravity - you don't think of the bedrock rules of your world until you're looking for a way to lock down the definitions of your world, the way De La Mar's team were. Once you have reason to ask questions, you know enough to ask the RIGHT question - in this case, 'how is all this weird shit happening when it hadn't been before???'