I installed Enigmail extension within Thunderbird. So, when I'm about to shutdown portableapps launcher a message is displayed that portableapps can't stop because dirmngr is still running.
When Thunderbird is shut down then GPGShutdown is called which properly terminates gpg-agent but leaves dirmngr running.
GPGShutdown should also terminate dirmgr. dirmngr can't even be terminated by means of gpgconf: .\portableapps.com\PortableApps\CommonFiles\GPG\bin\gpgconf.exe --kill dirmngr