The author of Notepad++ even said it, "It doesn't prevent your original notepad++.exe from being replaced by modified notepad++.exe while the CIA is controlling

The author of Notepad++ even said it, "It doesn't prevent your original notepad++.exe from being replaced by modified notepad++.exe while the CIA is controlling your PC." If CIA is already on your compromised machine and they want to target user of Notepad++, then they would just patched Notepad++ itself.