I call bullshit on that theory. There should have been multiple sailors on visual watch at various points throughout the ship, in the event that electronics are compromised. The good, old Mk II eyeballs are sometimes better than electronics equipment. If there weren't any humans actively watching for traffic, then the entire command ladder should be fired. It looks like that process has already begun, since that Admiral has been relieved of duty.
As a pilot, even though I may have fancy equipment on board that indicates traffic, I'm still making a visual sweep to confirm there's no traffic. I'm sure the Navy takes traffic watching duties seriously. And if there were sailors on watch and they were derelict in their duties, then they should be punished severely. I doubt we'll ever know the truth behind either incident.