I'll see if I can help based on my limited experience with some of your specific questions.
Core - Since it's going to be in a wiring closet and not a core/md hybrid, the hardware requirements are pretty general. Any modern computer should work fine. Personal recommendation would be 2G ram and plenty of space for things like additional hard drives and internal cards.
MD - Not all Atom based mini-itx computers are ION based, but the few that are should be perfect MDs. I've been using an ION based netbook (single core, 2G ram) for a couple weeks and after a couple tweeks it's been great. I have a dual core 2G Aspire Revo on the way, which should be fully supported and perfect for the job. Based on my testing with my netbook, the lower end single-core would work great as well but I wanted integrated spdif output, the extra 1G ram, and the dual core cpu can't hurt. The only limitation is hulu. Adobe has not released a hardware accelerated version of flash for linux, and it's starting to look like they will not for quite a while, if ever. If you want hulu on your MD (which is pretty slick), you need to step up to a desktop class CPU.
DishNetwork - This may be troublesome. I have heard that the Dish set-top-boxes support firewire. I used firewire a while back with the Comcast STB, and it was problematic (myth would lockup if you tried to tune an encrypted channel, then get stuck on that channel and lock up whenever you started myth). I believe those issues have been resolved. When it worked, it worked beautifully. Full HD picture, no performance issues, full control of changing channels and capturing video over one cable. If you can get unencrypted video over firewire on the Dish STB, this is the way to go. If not, do some searching here for methods of running HDMI over cat5 - some slick ideas for controlling the STB remotely and getting HD video to the TV (not PVR though, just watching live), but it does require a separate network cable so it may not be an option for you. It may be possible to use the Hauppauge HDPVR now. I don't think it's plug and play yet, but as a last and expensive option it should be possible to use for HD recording of analog component video.
I have not setup any home automation yet. I was leaning toward insteon because it's backward compatible with the plethora of cheap X10 devices, but it doesn't seem to be as well supported in linuxmce as Zwave. Beyond that, I can only suggest you search the forums for specific requirements.
I'll be adding a USB to rs232 cable to control my Sharp LCD tv. Hate to say it - search the forums, there are a couple specific models mentioned in other threads that are known to work.
Ripped BDs - I rip all my DVDs and convert them on my desktop before moving them to LMCE. To date I have bought exactly 2 BD movies - one I could not rip correctly (could not get forced subtitles), the other I converted to .mkv and it plays just fine on my MDs. 710 had issues with some .mkv files having green blocks growing in from the side. What format are your ripped BDs in? I'll see if I can rip a full BD movie and copy it over. Not worth the ~40G of space for a single movie for me, but I'll try to at least test it for you unless someone else can confirm/deny functionality.