By default, searches do not include deceased people. If you want to include them, add this Condition located on the Miscellaneous category tab in Search Builder with the Comparison Equal True.
If you are using the Condition Deceased Date, you do not have to add this Condition to that search.
Use Case - History
If you want to find the individuals that were enrolled in a specific org in the past you can use Was Member As Of and add this Condition to get the total count of those enrolled. Without this Condition, you would not have the deceased people included.
If you want to find those who were church members during a specific time frame, you can add this Condition to the search that looks for people whose Join Date was a prior to the end of the year, and whose Drop Date was not before the end of the year. You would also want to add the Condition Church Member Status equals one of and select Member and Previous Member.