Since Thunderbird 3 (or maybe before that), when you encounter an invalid SSL certificate, the GUI doesn’t even offer you to add an exception as in Firefox. Counter-intuitively, the same GUI than in Firefox is actually, available you just have to dig it through the menus. Here is a step-by-step tutorial with screenshots (had to do them for a doc, thought I’d share).
Go to Account Settings
In Security menu select View Certificates (alternatively, you can get there through Edit, Preferences, Advanced, Certificates, View Certificates if you have no Security menu here)
In Servers tab, hit Add Exception
Enter the address:port of the service you are using (without any protocol://) and hit Get Certificate
Hit Confirm Security Exception, and you're done !