There are still audio issues with Dolby Digital audio. The severity of the issue depends a lot on the audio receiver you are using, from what I've seen Onkyo's seem to take the longest to recover from whatever error is in the stream causing the drops.
As for your 2 HD outputs, DirecTV doesn't have that. What they do have is Whole Home DVR, where using the coax that connects the receivers to the dish are used for networking HD DVR's and HD receivers so they can view content between boxes. There is a $3/month charge for Whole Home DVR service.
The audio dropouts occur when hooked up directly to the TV either through HDMI or composite audio cables. How can people keep blaming them on AV receivers when they are there whether you use an AV receiver or not.