For the NSA to fully disclose their knowledge of 9/11, both prior and during would have exposed a number of things they were not ready to have disclosed. For example, their information taps were not just on foreign nations, but also the FBI and CIA. The NSA was spying on our own national covert agents and not disclosing this to the FBI and CIA. Assuming they had knowledge of the attack in advance, the only way they would be able to publicly acknowledge it, or even relay to the FBI or CIA would be to admit they were wiretapping other federal agencies. That alone would cause so much backlash for the NSA that they weren't willing to take that risk. They had to watch this whole thing unfold and were unable to stop it.

Having this knowledge means they probably had one or more of three possible scenarios happening:

• The inability to communicate with other agencies as so bad that even if the NSA tried, they simply might not have been able to effectively convince anyone of the threat without exposing their own methods.
  
• The NSA might have uncovered that one or more federal agency was involved in the attack, such as staging a false flag operation, and knew that exposing that agency might have far greater backlash than the actual event of 9/11.
  
• The NSA did relay the information but the other agencies simply fumbled so hard that it just turned into a giant clusterfuck. And that if the American public knew how incompetent those federal agencies were, that would be much worse than 9/11 itself.
  

In the end, the NSA probably chose a defensive stance and kept quiet so that their surveillance operations continued uninhibited for the upcoming war on terrorism and invasion of the middle east. Likewise, the federal agencies involved, under the direction of the executive branch, realized some of the mistakes made and took steps to improve inter-departmental communication.