I have struggled with validating certificates on N900 recently and this is how I understand it:
This will always end with error as you are not passing location of the certificates to the openssl command like in your next example. It has nothing to do with empty /etc/ssl/certs/ folder. Try it using some other Linux distro and it will end with the same error too.

There is nothing to be fixed.

Applications like links-browser or Alpine email client know the location of certificates because it's provided during compilation as one of configure script arguments: --with-ssl=path for links and --with-ssl-certs-dir=path (for Alpine).