The Documents folder on my Mac (macOS Sierra 10.12 beta) is not visible under my user in Finder. I can see the folder is there through Terminal
But in Finder, I can't see it:
I can see the folder in Finder under iCloud Drive:
This is a new feature in macOS Sierra. It allows you to put Desktop and Documents folder in iCloud Drive so you can access it in all of your Mac connected to that account and even iOS devices. You can disable it by pressing Apple Menu -> About this Mac, then go to storage and click Manage under Macintosh HD( or the name of your macOS partition) then in the iCloud part you can turn that feature off.
Check the "iCloud Drive" under iCloud in the Finder window sidebar. There may be a visible Documents folder there.
I had the hidden Documents folder too. It showed up in sidebar, but not in my user directory. I had to move all my files and folders within my Documents folder to a different folder, say on my Desktop, then completely delete the Documents folder using Terminal. sudo rm -r Documents/ As soon as it deleted, it was immediately recreated, and now visible. I then just moved everything all back.
While I'm not sure what the reason is (maybe a beta glitch or temporary decision), you should be able to work around it by using the Go To Folder command in the Finder and entering ~/Documents. Then drag it to the Favorites sidebar and you can always access it from there.