I would probably pick the parent folder.
And copy/paste from each of the symbolic folders, specifically the WTF folder from the copies.

That way, you'll have almost all of the toon/account specific configuration on the parent folder.
Run each toon, from the single folder to check it runs from the main folder.

IS Boxer has something called virtual files.
It will virtualize your config.wtf folder, so you can have different options on each toon, with a single install of warcraft.
The different options is the only real gain from the symbolic links.
And with virtual files, you get all those gains without having to mess around with multiple folders on patch day.