Maybe there was an over-reliance on signals intelligence and the terrorists were passing paper messages via couriers.
Indeed. There are a number of scenarios that would explain the intelligence failure without invoking some huge, self-destructive "deep-state" conspiracy. If there were such a conspiracy, given the monumental carnage and misery, someone would have revealed it by now. That's how I see it.
Your comment brings to mind an tale from the early days of the space race. It seems that ball-point pens would not work in zero gravity so the FedGov spent millions to design a writing device suitable for use in space. Meanwhile the Russians also discovered the same problem and solved it by issuing pencils to their astronauts.