The catacombs on Malta are surprisingly numerous and the highest concentration can be found in Rabat where you find four that are accessible to visitors. I visited two of them: The largest is the catacomb of St. Paul and it is surprising how large they are: After visiting a decent introductory museum you can enter the catacombs via twenty or more separate (modern) entrances, each leading to a seperat underground complex of various sizes. They are impressive but since there is very little decoration left after a while they resemble each other. But in some you can find inscriptions or carvings that give hints about the roman, Christian or Jewish religion of their owners. For a second visit I chose the St. Agatha catacombs that you can only visit with a short tour because they had several murals left. At the start you enter a large chamber with colorful murals but they are of later, medieval origin and have been vandalized by the Islamic invaders of the Island. More interesting though more modest were to paintings from the 4th century. 

When you are there it is certainly worth to visit at least one of the catacombs but they are modest compared to the already inscribed and more impressive complexes of Rome, Naples and Syracus. 

A combination with the old town of Mdina seems possible but I am not in favor of combining two weak proposals: There is no connection between the baroque citadel on the hill and the catacombs in the plain but the vicinity and there is hardly anything left of the intermediate epochs to connect them.