I’ve lived in NYC for over 35 years, up and down subways, Penn Station, Grand Central, 42nd St. and Port Authority, and never seen anything like you are describing. All I see are bored National Guard. Even the week after 9/11, I didn’t see what you are describing.
That was only one day at the 86th Street station in Manhattan.
If memory serves, there was a vague ‘threat’ that the FBI had repeatedly said was not to be taken seriously.
I remember that day quite well.