Pretty much the only advantage of multiple folders over a single folder is different configuration options for each folder.

For example you can have your solo play folder with every option cranked to the maximum.
With only the one account going, any computer capable of running 5+ accounts will be relatively smooth.

You can have another folder with most options down/off, except say viewing distance.
You then run the lead toon from this folder.

Have another folder with every option down as far as they will go.
Run the slaves from this folder and their tax of the system will be minimal.

Symlinks, mklinks, junction points etc, are getting the data from a single parent drive.
As far as performance goes they're not noticeably different from a single folder.
Symlinks etc or a single folder should be faster then multiple non-linked folders on the same drive.

I've heard if you have wow on two or more physical drives it can be faster then everything on one.
Because you're accessing the information simultaneously instead of one then the next.

If your software has virtual configuration files, then you can have all the benefits of separate/symlinked folders, but only one physical folder.

A single folder to patch is simple on patch days.
With multiple folders I have had issues in the past -- some patches were fine, and others have forced a reinstall which sucked.