Tom, for the sake of this discussion I am subscribing to the Nikumaroro hypothesis.
I have done some scuba diving, and perhaps my perception is distorted because I have not been diving in waters as pristine as those around Gardner, (though I have overflown Cuba and Grand Caymen on several occasions) but I have my doubts to whether an aircraft, even a shiny one like the 10e could be easily spotted at a depth of 400 feet.
I also am left to wonder why the castaways were able to live for only a relatively short time on this island. There are plenty of crabs, birds and fish to eat. If the campfire is indeed theirs, they were able to make fire, and with fire comes the ability to put together a small still for separating H20 from salt, cook food, and signal for help. It would seem by the time of the overflight mentioned above and the "recent inhabited" finding, they had indeed perished.
To me a logical explanation is that one or even both were injured during the landing. It has been speculated that because the surface of the reef was smooth enough to land on they could not have been injured. I have seen several accidents where there appeared to be little damage to the car, but the occupant was killed. Conversely I have seen several accidents where one would believe no one could have survived, and yet all the occupants did survive. There for I can in no way infer the continued health or safety of the occupants when involved in a ditch landing. Further, it would then imply to me that because of the short duration of their occupancy, that both were likely injured and subsequently perished from their injuries. It would also seem logical to my male chauvinistic mind that FN was more seriously injured than AE, and AE found herself having to attend him, and provide for both of them. Following this logic, FN with a head injury could easily have wandered into the ocean while AE was asleep, thinking he was walking into the front door of his house in the states. She awakes in the am, and he is gone. Another possibility is he perished, and she was forced to bury him, in which case, his remains could still be buried on the island.
This has likely already been mentioned, but my being new here please forgive me if I bring this up again. Being a dog trainer/handler it makes me wonder if bring a cadaver dog on the next exploration of the island might not be a useful addition.