I prefer to add mounting holes in eeschema as suggested by Rene in a previous post. One reason is if for some reason you need to delete unused footprints say because you have changed a connector, the mounting holes will get deleted too when you do an incremental update. When added in eeschema, they have a starting ref of H? so will have to be annotated and assigned a footprint. Another reason is if they have pads and if desired they can be connected to say the GND net. But usually they are isolated.