A reference to “John Smith, late of Bedford County, Pennsylvania,” probably means that Smith used to reside in Bedford County but no longer does. It does not necessarily mean that Smith was deceased. “John Smith, formerly of Bedford County, Pennsylvania,” means that Smith used to live in Bedford County, but that he no longer does.
Occasionally “late” and “formerly” may refer to a name used by an individual, such as “Karen Smith, formerly Jones.”
“Deceased” usually means dead.
“Late” does not have to mean dead. Sometimes contextual clues will make that obvious and other times they will not.