By all accounts I've seen thus far, this Mooney bounced off the water after striking water with the fuselage, in which case I would agree that he was far below prudent altitudes but bersonal minima are exactly that, personal. What's low over the water to you is likely not low to a seaplane pilot for example. With a low-wing 17.5ft (35 total) wingspan like a Mooney, it wouldn't take much of a turn and a swell to bury a wing tip and cartwheel the plane and you are absolutely correct about the hazards associated with the lack of peripheral cues and is more or less what I was getting at with my comment about "planning for swells."
Flying over open water is quite a bit different from flying over a protected harbor, lake or river because of the lack of visual cues (including boats) by which to gauge your altitude. You also have the additional challenge of dealing with swells of unknown height that you are likely unable to see or gauge from the air. While swells are typically fairly uniform, it is also not all that uncommon to have individual waves that are quite a bit larger than the one's preceding or following it.
For VFR pilots, VFR on Top is not an option.
To be clear, I'm not endorsing this type of flight but neither am I condemning it. I'm not here to judge others for their flying; if flying low over the water or scud running under the clouds floats your boat and tickles your fancy, have at it but do be aware of the risks and the "other considerations" you should give to such activity before doing so.