Root overrides all access privileges, so it is possible to read anything on the system. But root cannot impersonate another user and run as if it is that user, so it is not as simple as opening those mailbox files with Mail as root. I imagine the mailbox files could be copied over to root's Mail folder and then be read that way, however. Otherwise, the root user would have to extract the data from the files manually.
If you're concerned about the possibility of root reading your files, you may want to use FileVault (System Preferences: Security). Be sure to read up on it though - there are some issues with FileVault and it's a good idea to know how to handle those issues in the event that they pop up.