I have a linux server with postfix, the emails are delivered locally.
Would it be possible to protect the contents of the mail folders (using encryption or any other means) to forbid everybody (even root) to read the contents of the emails?
This is not possible in "classic" linux security model. Root always has all permissions. But there are some alternative security models as well. MAC or RBAC for example but you should be administrator to enable them on your server.