Well, I have a strange way of looking at scenes like that - I was thinking about all the complex computer programming and design that went into trying to make the waves look authentic :-).
But one thing that struck me as odd was that no buildings collapsed. You would surely think that the kind of force represented by those waves would collapse a lot of buildings and turn NYC into a pancake. It's quite possible that the filmmakers consciously decided they didn't want to create another 9/11, but it's equally plausible that making the city a pancake would have so obviously killed everyone in the city, including our heroes, that it was just not viable as a plot device.
You might remember that the 1993 attack on the WTC was supposed to cause the tower to fall horizontally towards the other tower, destroying them both. This didn't happen, and in the case of 9/11, the two towers collapsed with remarkably little damage to the surrounding area. In the case of a giant tidal wave affecting New York, I can't see the buildings not collapsing into each other, in a remarkable echo of was was supposed to occur in the 1993 plot.
The point many reviewers made was that the people who died were like ants and props, and you really didn't feel anything for them. My opinion was identical to the reviewers. There's something ugly about such a huge desensitization of death.
In thinking about your question with the tidal waves being echoes of 9/11, I didn't think about it at the time, but there were some scenes that did look remarkably similar. That's only in reaction to your question, though. I was more involved in the moronic actions of the characters at that time than anything else. It's likely, though, that the events are not comparable because The Day After Tomorrow was made on such a grandiose scale - even the World Trade Centre towers are pretty small compared to having the whole island of Manhattan as your canvas.
The plot was so poorly thought out and riddled with inconsistencies as to make even the special effects feel oddly moot. If your suspension of belief doesn't work for the plot, the special effects are likewise diminished for you. At least that's how I saw the movie.
Did that help?
D
Thanks for your comprehensive answer. I guess the whole production was so over the top in its fantasy, that the scenes didn't individually cause reactions of disgust at the open politicization, just dismay at the cheesy concept.