It's one of those tight rope walks that any entertainment media has to walk when dealing with a tragedy of such proportion.
you also have to consider that within the DCU you have Metropolis, NYC, and Gotham City all along the Eastern seaboard (typically somewhere between Virginia and New England and either in New York State or some fictional state)
by the time 9/11 occurred in our reality, both Metropolis and Gotham had suffered the Doomsday Rampage and the "No Man's Land" Earthquake, about 5yrs or so before hand. (Not to mention the vaporization of Coast City on the west coast in the Doomsday arc)
to insert 9/11 as we know it into those worlds would invite comparative statements from the DCU characters which would cheapen the true loss. also you need to remember that most Marvel characters operate in 'real world' cities while most, if not all DCU Heroes patrol fictional ones,
when Marvel did the 'Black Cover' Spiderman about 9/11 Stan Lee did a few interviews explaining it, and he stated that since Spidey and others are based in NYC that they felt the need to reference it in some form or another.
and it was the original Spiderman film, that had a sequence in the early teaser trailers that featured a helicopter getting caught in a spider-web between the towers, but from what i understand it wasn't an actual scene in the film, however the towers themselves were obviously in many background shots, and were removed digitally to 'be sensative' and my guess given our short attentions spans these days to avoid 'dating' the film as having been shot pre-9/11 since it only hit theaters the summer of '02
as to why it wasn't stopped, "Super or other wise (he) is just a man." (Darkseid JLU series), perhaops he was on the otherside of the planet, or even off-world, while Supes is based out of Metropolis he has been known to save everybody who asks, so there is countless places he could have been