The most safe method for removing the emanual popup is modyfing the 00000006.app file (the app file that has the HOME Menu buttons Wii Menu and Reset.)
Hey @mrt84 here's a modded version of 00000006.app file that allows to remove the emanual popup from HOME Menu on Flash WiiWare WADs! Link: http://www.mediafire.com/folder/aoiukku4ouxck/