I am using Gerald Garth Johnson's excellent book that has up-to-date historical research on this family -- The Biography and Genealogy of Captain John Johnson (Heritage Books, 2000).
John Johnson's children should not be a source of confusion. In the list of passengers arriving on the Arbella in 1630 were:
John Johnson, about age 40
Margery Johnson, 2nd wife, about 35 - 40
Children of Mary Heath, 1st wife and John Johnson:
Mary, daughter 16 years of age
Issac, son, 15 years of age
Elizabeth, daughter, 11 years of age
Humphrey, son, 10 years of age
Sarah, daughter, 5 years of age
Hannah, daughter, 3 years of age
John Johnson and Mary Heath had four additional children who were baptized and died and were buried in England. The church records support this. They were:
John (1618 - 1627) THERE WAS NO SON OF CAPTAIN JOHN JOHNSON LIVING NAMED JOHN WHO CAME TO AMERICA. THE HISTORICAL DOCUMENTS DO NOT SUPPORT A SON, JOHN JOHNSON.
Joseph (born and died in 1622)
Susan (1623 - 1629)
Joseph (born and died in 1627) Yes, it was a custom to name subsequent children after children who died in infancy and yes, Captain John Johnson and Mary Heath had two sons named Joseph, neither of which lived past infancy and who were buried in England.