MDaemon message files are always plain text format. Since the server is physically not accessible to any user and password protected, so the only person who has the access is the IT team in most of cases. There are alternative ways to protect it to make it even stronger.
MDaemon does not have any options to encrypt files on the server. However, You can restrict access to the server is the correct answer for this case.
If you have MDaemon running as the system account, you can hide the user/public folders using Windows permissions from all users except the system account.
If an administrator has access to the MDaemon server, the security permissions could be changed. If this is occurring, You should look into properly securing the Windows OS running MDaemon from any unauthorized access.