The greatest defensive measure are the many layers of concealment on all things, including the small port. This prevents the base from being detected by prying eyes.
Should this not be enough, the underground storage could easily be converted into an easily defendable fortress.
In order to get a foothold in the harbour town, for "completely legal trade", the agents of dragonfly deliveries thought it best to have a forward base of operations. The island was acquired through legal means, but under odd circumstances, should one ever look into it.