Hmmm... I wonder, with Venice, it would be interesting to use that arrangement as well, but put the port facing the mainland, blocking a strait that is the only access to the island. The idea is, this will make it more likely that an AI controlled Venice that keeps a fleet in port will block the strait and make it impossible to attack the city.

This is sort of like the arrangement in EU2, where Venice was only accessible via a strait, and that strait could be blocked easily by the Venetian home fleet. It was an excellent way of preserving the independence of Venice despite its small size and manpower.