Looking into it, it seems that the /etc/ssl/certs/ca-certificates.crt file is just a concatentation of all the certs found in /etc/ssl/certs/. So to generate this file I simply ran as root:
cat /etc/ssl/certs/* >> /etc/ssl/certs/ca-certificates.crt
Easy as that. Now my Funambol connector for Thunderbird (using curl) doesn't complain and then fail to sync.