Ok, after consulting with a colleague this might be an issue with kwatchgnupg. Which is the tool started when you click on Tools → “GnuPG Log Viewer” in Kleopatra. (But it can be started on the command line, too.)
This then writes the line log-file socket:///home/user/.gnupg/log-socket in all existing .conf files in you GNUPGHOME apparently and does not delete them again when logging is stopped.
Did you start kwatchgnupg in the past? Maybe unintentionally
This is usually only annoying, as the message is only a message warning you that no log can be written to the socket and logging will then fall back to STDOUT.
But if you have kwatchgnupg or watchgnupg running, you will get all dignostic output there and not in your terminal. Which is very confusing. But gpg should do the operation anyway, e.g. encryption. But in your case is was a verification and that result will only appear in the log viewer. Do you have one running? Can you confirm you see the output there?
In any case when you delete all the log-file lines in your configuration files in GNUPGHOME which point to a socket you will see the output again on the command line.
Kwatchgnupg has not changed in some years AFAIK, so I’m not sure if something else has triggered some change in the behavior. Can you point to a specific update after which this started to happen?
Anyway, we will think about how to improve that irritating behavior of Kwatchgnupg in the future.