I know this is an older post but I encountered this exact same scenario for the exact same reason. Posting the solution that I found incase someone finds this thread via google as I did. I have an external HDD that I sync some files to using rsync and the top level folders were showing up under /mnt/user/<folder name> and were directly linked to the directory in the pool drive.
The fix for this is stop the array and in the pool settings set "Enable user share assignment" to "No". Once this was complete the rsync works as expected and folders dont show up as shares.