Only Network Administrators can see deactivated organizations when running reports. Other users will see the active organizations they have access to.
The list of Program Types already includes deactivated programs. As long as there was data recorded within that program at some point, the program type will show.
To enable a report in your user profile:
Go to Administration, Users
Click on the orange edit icon beside your name
Click on "Intake-Specific"
Click on "Edit User" on the right side
Go to the Reports tab
Check off the report
Save your changes