Hi Fishypete,
In ancient times people were introduced or mentioned with reference to their parents. The parents just by being of an older generation would be more known than their children. People did not really used last names as we do today, so it was a way to specify which ‘Joseph’ also. So, Jesus was not only the son of Joseph but the Joseph of Nazareth to be more specific and so Nathanael would be better able to know who exactly it was that he was referring to.
In Plato’s writings we read - so and so the son of so and so, also. Even today, actually, in some Spanish countries, people will speak of someone ‘Maria’ the daughter of so and so - to specify.
I checked some Bible references and have found nothing that is suppose to be negative or whatever by referring to Jesus as the son of Joseph from Nazareth.