No, I doubt Disney would touch the ending to add the 9/11 events, although this was and is a powerful statement to Americans, the show is designed to show the talent, diversity and promise of America, rather than the efforts of the jealous maniacs who try to destroy it, I take your point, but just feel it might tarnish the show.
However, if you look in the foyer of the show there is a charred American flag that Disney brought from the site with a picture and message.
I think when Disney finally has some money free they might update the recording to make Ben Franklin say 21st Century and also many of the animatronics need refurbsihment, fans of the show will see at the very end Ben and Mark go to shake hands, and miss. Now, they never did actually touch and this is a very difficult effect, but just recently they have been missing quite a lot!
Hope this helps.