Nope, but you can use the file placement limiter to control which drives are storing duplicated and unduplicated files. And if a drive is only storing duplicated files then you can exclude it and only backup the other drive(s).
The problem with changing the folder structure is that there is no master version of the duplicated files so placing them in a separate folder would mean that both copies of a file would be placed in that separate dir and thus by your idea (as I interpret it) both version of the duplicated files would be excluded from backup = no backup at all.
I would suggest you look at third party backup solutions. Either those that include de-duplication in which case it doesn't matter that you backup duplicate files or file level backup tools that you can use and backup the Pool drive (and not volume level like the built in server backup tool)
I personally use Crashplan which fits my needs but your's are probably not the same as mine