Ok, why the devs doesn't want normal users connecting to Nintendo WFC? Because the code is experimental and isn't fully implemented, so, this is why the code stay in a separate branch. We, normal users, should avoid using Nintendo WFC, if a lot of users starts connecting, Nintendo may block Dolphin in their servers and then the developers won't be able to finish the work, and after all there is no guarantee that the code will be finished at all...
This can make people thinking that they can use cheats and mods when playing online in Nintendo WFC, doing this will probably make Dolphin getting several troubles with Nintendo after all. So, if you like Dolphin, the best you can do is avoiding this branch until developers finish it and merge to master or wait until they say that the branch is safe to use (but probably will never be -- this makes me remembering what happened to DeSmuMe when the online connectivity were implemented)...
It's actually not really that big of a deal anymore. The Wii-Network branch and the needed files to use the online functionality are going to change in the future.