The plus side is that GnuPG by design has a relatively limited attack surface. It's tough to conduct a side-channel attack that requires thousands of message stimulus-response tests to get a single key or message bit, given that each iteration of that attack will (in typical GPG usage) require manual intervention.
As long as your crypto isn't "online", GPG is still a pretty safe bet. You can't say the same thing about a lot of newer crypto libraries.
However, if you're doing something like encrypting a session cookie, you should use Nacl, not GPG.