The WD utility doesn't run on WHS (or at least it didn't when the drives first started coming out). Given that WHS storage pool drives only have one partition, I don't see why you couldn't use the jumper method to have the drive realign sectors automatically.
I don't have much experience with Hitachi drives, so I can't comment on their reliability.
I don't have much experience with Hitachi drives, so I can't comment on their reliability.