That is because emelfm2 has an existing desktop file which is used in 2.x if present, instead of the tc2freedesk utility in base making desktop files out of tce.menu/tce.icon files if one is not present during extension loading. Emelfm2 and many others have the X-FullPathIcon to support old WM's, but that does not create multiple menu entries like tc2freedesk does.
This is one of the exact problems that would have been seen with many extensions in the 3.x repo if they were not converted as they were. I can adjust the 2.x extension to have the multiple menu entries.