The use of stealth helicopters in the game is most certainly a reference to the brief 90's buzz word "Black helicopters" used by conspiracy theorists and UFO hunters. The idea back then was that the US government, or some secretive organisation within it, was using silent and black helicopters to spy on or abduct people. In Deus Ex, sensationalist conspiracy theorist paper "The Midnight Sun" echo this idea, while at the UNATCO HQ you can actually find UN manuals talking about these type of helicopters.
The twin towers are not the only thing missing from the NY skyline in the game. In an interview it was explained that they were saving in on texture memory by using a simple mirrored texture for the lights along the edge of the water. Still, it IS an eerie coincidence that the game about a future (exploitation of the) war on terrorism was released a full year before the real thing kicked off.
Deus Ex was actually just a collection of popular and more obscure conspiracy theories, names and iconographies reworked into a single story. They conjured up a sense of conspiracy and dystopia that no other game has really managed to do right. Many have tried but none were as ambitious and subtle about it as the original Deus Ex. Most dystopian future stories take the "The world is run by corporations" route while Deus Ex had a more realistic angle where "Rich businessmen turned poiliticians employ private mega corporations at exorbiant costs to the reserve and tax payers".