There was a conscious effort to remove the Twin Towers, post 9/11, but they still pop up from time to time.
Them getting knocked over, by a tidal wave, was the money shot in "Deep Impact."
I remember Snake Plisskin landed a glider on one in "Escape From New York."
In 'Armageddon', made in 1998, the Twin Towers are hit by meteors in almost the exact spots as the explosions occurred on 9/11. You won't see that part of the movie on most TV channels today because they edit it out.