GPG Mail not in Manage Plug-ins list after installation or doesn't remain active
What you are seeing is a bug which can occur if during or after installation of GPG Suite System Integrity Protection (SIP) is deactivated.
To fix this problem:
- Close Mail.app
- Open System Settings > Security > Privacy
- Enable Terminal under Full Disk Access
- Restart Terminal when prompted
- 
Copy paste the following command into terminal and press Enter: sudo rm -rf ~/Library/Containers/com.apple.mail/Data/DataVaults
- 
Open Mail 
If you are seeing the error "Operation not permitted" temporarily disable SIP and repeat step 5.
Make sure to re-enable SIP once the steps have been executed.
Hint for macOS 10.15 Catalina users: You do not need to disable SIP. You can simply remove the folder in question from Finder.app to resolve this issue.