That's what I thought when I first saw the film.
It seemed remarkable that no one (not even
his son) realized that old Bootstrap Bill was
alive somewhere on the bottom of the ocean

But on the DVD audio commentary, the
filmmakers spoke at length about this...

They explained that since Bill was dropped in
the deepest part of the ocean, and even
though he was still alive, the pressure had
mostly likely crushed the poor guy to a pulpy
pancake. So when the curse ended, he was in
no condition to save himself.

Of course, the "explanation" rather sounded
as if it had been created after the fact. And a
creative writer could certainly find away around
it anyway. Here's hoping!