The Wikipedia article says that he was murdered by Beckett's aid Mercer sometime when he was out with Beckett, Mercer, and Norrington when they were on the Endeavor while he was hoping to find Elizabeth. He must have been murdered at sea, or else he wouldn't have been found by his emotional daughter in Davy Jones' Locker when Jack Sparrows crew was going to rescue him. He must have died just before Jack's crew got to Davy Jones's Locker because he was one of the people in the longboats among the recently deceased. Poor Elizabeth :( Her life really really sucks. I feel bad for her :(
No, but she was separated from Will and can now only see him once every 10 years.
John Weatherby died in 1948.
Roy Weatherby died on 1988-04-04.
Charles Alfred Weatherby died in 1949.
Charles Swann died in 1960.
Jack Swann died in 1990.
Sidney Swann died in 1976.
Edward Swann died in 1945.
John Swann died in 1793.
Michael Swann died in 1990.
Donald Swann died on March 23, 1994.
Thomas Swann died on 1883-07-24.