Maybe some deck guys can help me understand how this happens:
I read elsewhere it happened during taking on or dropping off the pilot. How can a guy fall overboard in broad daylight…in a fairly narrow body of water (St. Lawrence Seaway) and not be seen again?? Chopped up by the prop?
This one says no life jacket, 6C water:
so not much chance of survival anyway, but what happened to the body?
Rigging a pilot ladder, particularly one with a combination accommodation ladder is fraught with danger and risk. There are too many types of boarding arrangements available to know for sure what this particular vessel was using but I have seen wire ropes fail, shackles that weren’t tight enough, and cracked steps on a Jacobs ladder.
If I were speculating, I would guess that this officer may have walked down to the end of the accommodation ladder to stand right at the Jacobs ladder to meet the pilot and was not wearing a safety harness and safety flotation vest. That would put him over the side of the vessel with no back up in case something went wrong. Something obviously went wrong.
As for his body not being recovered. It’s the Saint Lawrence seaway and the water temperature was bitter cold. Cold enough to shock your body into gasping for air as soon as you hit the water and you submerge from the fall with no life jacket. Either that or he was knocked unconscious. Again, just speculating.
As you mentioned, it is entirely possible to sink right to the bottom in cold water if your lungs are full 
…not empty?
Full 'o water. some people (me included) sink in fresh water even with air in the lungs.
…you must have been fitted with some very heavy implants…
Water in the lungs requires to have emptied the lungs before (of air)
You need to grow a thicker layer of fat and jokers will call you Bob.
Fresh water is overrated anyway. 
I was born and spent my early years on the banks of the Saint Lawrence. Every winter during the Quebec winter carnaval there’s a canoe race from Quebec to Levis.
Update on the main page regarding this tragedy. Apparently the Canadian authorities believe the second officer may have been engaged in lashing operations when he fell overboard. I had never heard of a port not providing lashing services before this. In my experience, it is never acceptable to leave the berth before the cargo is secured. Sad that a man lost his life because of this bullshit cost cutting practice.