The missing IR port and the lack of inclusion of an Apple Remote on the Mac Pro actually lends credence to a previous rumor...that Apple was working on new displays with built-in iSight and IR sensor.
Those displays could come with the Apple Remote, and give Mac Pro buyers a little incentive to go with the Apple display instead of a model made by a competitor. For a premium over the Dell displays, you end up with iSight and Front Row and a better looking match to your Mac Pro.
With the price drops, I am guessing the are hoping to clear inventory. New displays by the end of the year is my guess. It's not that urgent that an Apple display include iSight and IR sensor today. But by the time Leopard is out, Apple will want to show off the updated Front Row and iChat stuff on all the machines...including the Mac Pros.
Just a guess...