i was under the impression it was excluded because it would over complicate the war at hand. also, to mention it, at least in canon in 54, it would have to simply be a side note that isn't even relevant to the plot. if kaa did try to tackle 9/11, at some level, she would have to take a stance on the war. my memory of the series is a little faded, but i don't really recall her taking too many political stances, especially on something sensitive like that.
on the other hand, what might prevent the attacks if the yeerks really had invaded?
that's a complicated question. would the extremists hatred for america be diverted due to a bunch of slugs trying to come in and take over out entire planet? who knows. would it be possible to attempt to lay all blame on the yeerks for the injustices america performed on the middle east that gave rise to the extremists? i would guess no.
the issue of oil, one of many reasons they hate america so, might become a non-issue. if andalite technology made it possible for the globe to no longer be oil dependent, then the middle east wouldn't have to worry about america's hand in their oil industry. then again, if the globe is no longer oil dependent, what would the middle east have to export? i suspect that the inflow of technology from the yeerks and andalites would throw the globe through a bit of a loop while we try to figure out exactly which countries are going to have the ability to produce and trade energy. if each country theoretically became energy independent due to new technology, there would still be issues of trade. what exactly is the middle east going to sell to america? other than oil, the largest commodity (i think, not positive) in some places are drugs. i think the global economy would be thrown into a giant mess of uncertainty until the dust settles and each country figures out what they are going to export/import.
would the extremists have attacked the andalites or yeerks instead?
maybe, maybe not. the people that orchestrated 9/11 did not simply react in a knee jerk fashion (it is irrelevant here if america did react in such a manner as a response). they have a long list of injustices that they felt needed rectifying. i think they might not have attacked the yeerks or andalites and would have waited to see what the future holds with the aliens in the picture