You will want to take a copy of the /var/opt folder - this can then be restored in the event of a disaster! There is plenty more info on Scalix backup in this excellent thread:
You may want to include /opt/scalix as well. It is the static location of some of the server and configuration files. Depends on what your backup scheme is, but just a suggestion.
And yes, the mail store is all in /var/opt/scalix by default.