My guess is no (at least for Boot Camp partitions formatted as NTFS), since by default Mac OS X cannot write to NTFS partitions (and I'm guessing that SuperDuper uses the basic OS APIs for writing to disk). For FAT32 partitions, SuperDuper may indeed work fine, but I haven't tried it.
What SuperDuper would need to do to clone NTFS partitions would most likely be to perform a block-level copy, which I don't *think* it currently does.
I look forward to hearing from Shirt Pocket Software about this though. I hope adding full Boot Camp partition support is on their To-Do list!
