I also remember a short, wordless promo for the ninth season that simply showed Sipowicz standing by a waterfront and staring at the WTC-less skyline with a look of hurt and anger. I remember thinking that that was one of the most powerful little clips I had seen about it all at the time.

There was also a season 9 episode about a woman who was though to have died in one of the towers on 9/11, but in fact was not there, and ended up being murdered elsewhere, with her body being discovered later. I remember Medavoy telling the husband something to the effect of "we have reason to believe that your wife did not die at the World Trade Center".
I will have to go back and watch that. I don't remember it on Blue, but Law and Order had an episode just like that too.

Sipowicz is in a particularly crabby mood, and a fellow detective follows him into the pisser to give him an attitude check.
In fact, it was Charlotte Ross' character who did that (I can't remember her character's name, well that happens after 11 1/2 years)
There was also a season 9 episode about a woman who was though to have died in one of the towers on 9/11, but in fact was not there, and ended up being murdered elsewhere, with her body being discovered later. I remember Medavoy telling the husband something to the effect of "we have reason to believe that your wife did not die at the World Trade Center".

I've got a ways to go before the series goes to 2001. Was 9/11 and the WTC towers coming down ever addressed on NYPD Blue?
It was addressed early on in 9x01*, and several times throughout the season in varying degrees of scale.
*Sipowicz is in a particularly crabby mood, and a fellow detective follows him into the pisser to give him an attitude check.