Yes, that would have been the 1 train at Cortlandt St. The only other train in the lower level of WTC was the PATH from New Jersey.
Yes,I’ve been there more recently and couldn’t help but notice all the signs leading to the PATH train not far from the Post Office and the Episcopal Church that was damaged by the falling structures (Saint Paul’s?).
One entrance was next to Warner Brothers Store.
http://toolooney.blogspot.com/2007/03/nyc-flagship-warner-bros-studio-store.html