This seems to be the same behaviour I experience. For me, suspend to disk works the same as suspend to RAM.
So this strengthens my suspicion that the AppServer somehow gets "out of tune" with the core during long periods of sleep. I'll see what I can find out, but I suspect we need to have someone with a better understanding of the AppServer/DCE router stuff to look into it.
Regarding debugging the suspending, I haven't done it myself, but I suggest you read the s2ram article linked from the wiki suspend article. From what I understand, it is often a buggy driver that causes suspend/resume to fail.
I suppose that by "the MD device itself" you mean the LinuxMCE/Orbiter part? (The required software packages are already available in Ubuntu, so its just a matter of installing and configuring them).
As far as integrating it into the floorplan and suspending the MD via the Orbiter (and other similar uses), I suppose one would need to have a DCE command to tell the AppServer to suspend the MD, and to add a suspend button to the Orbiter power menu, and also add a way to suspend a device from the floorplan (I see there is already a power button on the floorplan, what does this do?).
I have no knowledge about the AppServer/Orbiter, so I wouldn't know where to start such an integration, but I am a C++ programmer (rather, I did some C++ a couple of years ago) and I would probably be able to do it, given the right amount of time