The very short answer is that, since we don't know what they called themselves, these are names that archaeologists use to designate different cultures that lived at the same site, usually separated by physical layers.

The issue with giving them distinct names (other than the previously mentioned "we don't know how they referred to themselves--which is kind of a big one) is that it could also cause confusion if the same culture is found to have inhabited other sites (or theorized to have done so) -- wherein Naqada I is also suspected to be the same culture as Abydos II and possibly Hierakonpolis III (I'm making these names up).