Quick workaround: add your own CA cert to your iPod. If you have your own WebDAV server, then you have your own web server, right? Copy your cacert.pem file to your web server's root directly, load
https://www.example.com/cacert.pem in your iPod's Safari, and it will open the security manager. Tell it to install that cert and voila! Your sync problems (and the similar warning message when you connect to your self-signed mailserver) are magically gone forever.