Looks like they check to see if the cert issuer is a trusted root CA and then they check that the subject name is "Notepad++"
https://github.com/notepad-plus-plus/notepad-plus-plus/commi...
https://github.com/notepad-plus-plus/notepad-plus-plus/commi...
If CIA is already on your compromised machine and they want to target user of Notepad++, then they would just patched Notepad++ itself.