These user folders in the Start Menu are special folders with a symbolic link that keep them connected no matter where the true folder location actually is. Think of it as just a shortcut that points to the actual user folder.
If you do not want you user folders included in the libraries, then you are good to go. If you do want them in there, then you will need to include the D:\My Pictures user folder in the Music library and so on for any other user folder that you moved. The tutorial below can help show you how to if needed.
Library - Include a Folder