macOS Sierra saves space in the hard disk by moving unused files to iCloud and leaves some kind of symbolic link behind for users to find those files later.
I suppose Hazel will not be able to act upon those files. Or will it?
I like to keep my hard disk tidy and clean. In my workflow, Chronosync makes a daily copy of files to a remote share. Hazel deletes files and folders that have not been opened/modified in more than 2 months. This is how I have kept my files neat and tidy.
If Hazel does not act upon the files moved to iCloud, I suppose many workflows will be broken soon.