Do they really have an underground base where they can park the submarine? Really?
Benefit. Protect the identity of individuals who visit the island, but don't want record of it (like the LE plane logs)
Interesting information about Water Island:
During World War II, Water Island served as an Army base to protect a submarine base on St. Thomas. Then the Army’s Chemical Warfare Division used the island as a laboratory for poisonous gas and chemical agents.
So there could be infrastructure left over from WWII or upgraded on St Thomas or Water Island to facilitate covert submarine trips back and forth to Little St James. It could have been kept under wraps for the simple reason that the infrastructure was already there.
I have a feeling James Biden's property has something to do with the facilitation of covert travel either trafficking or VIPs to Little St James via submarine.