Here's a screenshot of the World Trade Center from the cockpit of the airliner:
Or maybe they saw it but had a good reason not to mention it that was also given in the show:
The Cold War's over, John. But with no clear enemy to stockpile against, the arms market's flat. But bring down a fully loaded 727 into the middle of New York City and you'll find a dozen tin-pot dictators all over the world just clamoring to take responsibility, and begging to be smart-bombed.
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