OK, so I think I’ve figured it out - I had a brainwave and tried to use occ to update the market apps, to see if that gave me anything more sensible as an error, and I got this:
No marketplace connection: cURL error 77: error setting certificate verify locations: CAfile: /var/www/owncloud/data/files_external/rootcerts.crt CApath: /etc/ssl/certs
I searched for that error on the forums and found this - deleting /var/www/owncloud/data/files_external/rootcerts.crt and restarting my container fixed it, I no longer get the warning, and I am able to update apps again from the marketplace.