The second zone in most receivers and processors is basically a separate analog audio pre-amp. Doing more requires duplicating at least a DAC and possibly much more - you could handle up to PCM stereo if the second zone had its own DAC, but to go beyond that would require a separate audio processing chip for the second zone (decode DD, DTS, etc. and transcode down to PCM stereo to feed the DAC). Second zone video is often handled similarly (composite output requires composite inputs, component output requires component inputs) for the same reasons. That being said, I can see where supporting digital audio into a second zone could be pretty handy for some users. It could be done - it's just a matter of cost.

I don't know that I've seen any products that offer HDMI into a second zone yet. Multiple HDMI outputs typically feed two separate displays in the main zone (flat panel for normal use and front projector for movies, for example), while the audio goes to the same place either way. For your application (TV for general purpose viewing and projector with motorized screen for big movies), that's exactly what you'd need. Audio would go to the pre-amp outputs no matter which display you're using, and you would just toggle between the two HDMI monitor outputs.