This is all about simple economics. The number of customers who would pay the up-front lease fees for an HD receiver, pay the monthly HD access fees, and then connect it via to their TV’s the lowest quality SD outputs is very, very small. I understand there may be good reasons for doing this, like connecting a second “slave” TV or just preparing to upgrade to HDTV and starting with the IRD first, but it’s just not something that is normally done. Even if the RF modulator circuit only cost an extra $5, why spend that when 99% of them would never be used?
As for leaving the composite and S-video connections, a large percentage of those may go unused, but without them there would be no way to connect an SDTV at all. Also, many customers use them for recording onto other media like DVD, SD video capture cards on their computers, or even (gasp!) VHS.
Deleting the ATSC tuners from the H(R)21 series was done along the same lines. As D* continues to add more and more HD locals, fewer people will have any need at all for this. They may miss some local HD content, like The CW network, PBS and the secondary channels, but few people will worry much about that. I am sure D* monitored how many people were actually using the ATSC tuners and eventually decided to drop them. For those that do feel they need OTA, D* does have the AM21 available and I doesn’t seem to be too hard to talk them into giving you one for free. If you have a good reason.