A 50 cal can do a great deal of damage to small boats and aircraft if maintained properly and crew trained.. Granted they failed miserably in testing as quad mounts on Essex class carriers but more due to failure in maintenance and use.

If your sailing up on a docked U.S. warship and your small boat has 3-4 inches of armor plate yes the 50 cal user is in trouble. No armor plate and the typical fiberglass hull/fuselage will be torn apart by the 50 cal rounds used in short bursts, not to mention what the round will do to opposing occupants. The many Japanese planes on the sea floor of the Pacific will attest to the 50 cal effectiveness.

But really if you had the choice to fit a 50 cal or 20mm upon your craft who would not take the 20mm? In this case the USN chooses the 50 cal for the reasons Ralph lists below.