Assets are not included in the process which helps a lot, it still requires the original ROM to compile a ROM. Nintendo has heavily went against PC ports, even as far as videos about them on YouTube, but never even attempted to touch the root decomp projects for various titles. Later games you can get into more trouble because EULAs or on screen warnings started restricting reverse engineering, as well as DRM mechanisms which are impossible to reverse engineer without being implicated as also advertising a way to work around them.