This has been an issue for a while, but today there has been word from a developer about how the Steam Workshop downloading should be-

[LAR]Sebastiaan [developer]
@Isildur - Wildstar:
The game should move the file to the correct folder if you open up the mods menu. No need to do this manually.

http://steamcommunity.com/sharedfiles/filedetails/comments/295388152


Subscribing to a mod and opening the Mods menu in-game still does not download/move anything (except Cow Simulator) automatically. My most recent test of this has the mod I subscribed to still sitting in it's userdata folder, unviewable in the game.