untested, but:
- importing certs in the settings GUI of the N900 drops them in /home/user/.maemosec-certs/ssl-ca/ (filenames are hashes, they are supposed to be like this and it's nice the GHUI does hashing)
- my syncevolution config has "SSLServerCertificates"

As such I'd try first to just import the cert, if after importing and seeing it under /home/user/.maemosec-certs/ssl-ca/ syncevolution does not pick it up it may be useful to open a bug as that is the system's default location AFAICT.
To tide over, next try would be to set the directory in the syncevolution config and as a very last resort the certificate itself.

I will not have time this week to test it, but if the above seems daunting, do tell and I'll try and squeeze in a testrun next week (while that will be against a private funambol here, for SSL testing this should be OK)