To make it very simple the agrarin Maltese are the original People that arrived from Sicily in the repopulation project during the Aglabide (Moors/Arab) period who spoke Siculo Arabic probably like the area they came from in Sicily. (i dont think there is any record to who and were in Sicily these people came from). These people would have started to first Villages that later formed other villages as the population increased Adding to this population later came the settlement of barons that divided all the land between them but payed tributes to the king of Sicily, thus creating the 'universita' which was the sort of parlament based in Mdina (citta nobile). This was the time when the Island saw a resurgence of Aragonese garrisons to guard the Three Castles. That is Mdina, Gozo (Citadella) and the one instead of present day fort Sant Angelo. at the harbour entrance. (there was only one small town Birgu at that time as population preferred to live inland for safety.
With the arrival of Knights they decided to increase the population around the harbour and made Birgu their home (and not the medival town of Mdina). Here started a great industry in building ships (the Knights were famous for) and became richer through piracy. This attracted a new population and new immigrants. There have been numerous marriages from now Latin speaking Sicily, Italy and also France, and therefore created a kind of new society compared to the people who lived in the Countryside. This new society kept on growing with eventually the building of Valletta (after the victory of great siege of 1565. Today the whole harbour area has become like a big town mainly dominated by these industrial kind of people living on Maritime trade (compared to the Maltese living off agriculture and later proved to be good builders in the use of stone)
In my opinion these were like two different societies (kind of city people and country people). Even the language was spoken differently. People in the Country are still very faithful to the Siculo/Arabic with heavy and harsh accents, but People round the city has latinized much more the language and later Anglasised it (through the British rule) albeit still very semetic in its structure. If one looks well can also see differences in Phenotypes between these two societies but of course they are all termed Maltese.
