As for the matrix, I think that boils down to "Money, money, and.... money".
Business has to go on, and for that to happen, you need communication. Which means the matrix. Make people jump through 30 hoops to do a transaction (no matter where they are in the world), and they get annoyed and take their business to a sprawl that doesn't make them jump through those hoops..... which puts a dampener on your whole "Manahatten is the Corp center if the world" spin.
Besides, the 'new' wireless matrix protocols make hacking an elite field that only a relative few can do now. (G.O.D, the return of Decks, limitations placed on commlinks.)
<Remember the old security addage: "A lock keeps honest people honest".>