I'm not real up on file systems and drive architecture but the gist that I got from various threads is the physical sectors not lining up with the file system doohickeys is suboptimal. I don't think it's a functional problem, I think it's a performance problem. But maybe I'm wrong... if I were right, I don't understand how RAID could affect things negatively.
The new sector size issue has nothing to do with RAID, new sector size only affects pre vista windows system (that requires the disc to be re-alligned before proper usage), and that has nothing to do with the DNS-321.
The real problem is between RAID and all the WD-Desktop drives (not only EARS), in a nutshell, WD-Desktop drives will enter what they call "deep recovery mode" upon a failure to read a given sector, this process (similar to a scandisk) will try to recover whatever data on that sector and will mark the sector bad and move the data to someplace else. This recovery procedure might take up to 2 minutes to which the disk will appear unresponsive to the outside world.
Now for RAID side, the RAID controller inside the NAS (be its DNS-321 or any other), as per the RAID operation a disk is deemed unresponsive if it fails to communicate for 7~10 seconds, unresponsive disks are dropped from the disk array (which are typically more than two).
So the problem as can be seen clearly, any WD-Desktop disk that enters a deep recovery mode while inside a NAS with RAID enabled, will be incorrectly considered a failure and will be dropped out of the RAID array. This is not a correct behavior especially if the data can be accessed from other disk (its RAID), the disk doesn't need to attempt to recover the data but the disk has no idea its running in a RAID array, the RAID controller shouldn't drop the disk because its still functional .. but the RAID controller has no idea that the disk is still running. end result is a very unstable (yet functional) NAS.
Check
forums.dlink.com/index.php?topic=12483.0 for problem that was caused due this very same issue (not sure why didn't anyone in the thread point to the reason though).