I'm guessing that Alexander Scott is alive in 1841 and the reason the family can't be found is because they are living in a parish whose 1841 census returns have been lost.
According to SP these are the parishes that are missing
Abdie, Fifeshire , book has no entries
Auchtermuchty, Fifeshire , book has no entries
Balmerino, Fifeshire , book has no entries
Ceres, Fifeshire , no book
Collesie, Fifeshire , no book
Creich, Fifeshire , no book
Cults, Fifeshire , no book
Cupar, Fifeshire , no book
Dairsie, Fifeshire , no book
Dunbog, Fifeshire , no book
Kennoway: Only the enumeration book for Markinch has survived
Kinghorn, Fifeshire , book has no entries
Kinglasie, Fifeshire , book has no entries
Kirkcaldy, Fifeshire , book has no entries
Abernethy: Enumeration book for people living in Fife missing
Arngask: Enumeration book for people living in Fife missing