I don't have a Wii U, and I don't deal in Wii U stuff, however: One of the reasons why I was asked to change it from simply /homebrew/ to /homebrew/3ds/ was because people share SD cards among their Nintendo devices (apparently?..), and so having a /homebrew/ folder would make zero sense when viewed on a Wii/Wii U.
So the current paths allow Wii U to gather things up in their own folder without cluttering the SD root with another folder, which is pretty great since it's like many birds with one stone.
EDIT: To make it clear, I wasn't simply asked to change the path, it was more other devs and I had a talk about this and decided on /homebrew/3ds/ where as /homebrew/ was my initial idea without discussing anyone about it.