Mary Ann could well have died giving birth to William according to FreeBMD - 1846/1847
in 1861 census, John is still alive living with Sarah A and William Henry but there is an additional son Jonathon 11, and daughter Amelia 4......!
1871 has John, 71 living with Sarah Ann Vane - their is no husband to Sarah Ann but she has amongst her children an Amelia aged 13.........gone off track here slightly........