Though also over water, JFK jr.'s accident is a rather different loss of awareness. He should have been trained to recognized that in that environment, not only is the water not usable as a "surface" reference, there simply is none. You are effectively not flying VFR anymore, and must recognize that, and fly with reference to the instruments, even though you are still in VMC. No one would think to attempt to fly 50 feet of the water, at night, using the surface of the water as the reference.
Over glassy water, you are flying in decent if not very nice weather, with the surface in clear sight. But, it is not a suitable reference for establishing altitude within 100 feet. It is not a matter of seeing the bottom through the water, it's the reflection on the water which makes it difficult to judge height.