Disk encryption only protects against physical theft of the drive, which is not the primary concern with most servers. If a server is up 24/7 and I hack into it, it doesn't matter that the drive is encrypted since I have access to the decrypted files anyway. Encrypting incoming emails works because the mail server doesn't really care what the content of the email is, so decryption keys don't have to be stored on the server.
Can you give some more information about your setup?
In which phase to you encrypt the email, what tools do you use, etc.
Just use a procmail rule to call gpg on every incoming email before it's stored using your public key, then your client (configured with your private key) can decrypt every email as normal.
Here's my over engineered setup:
https://github.com/jakeogh/gpgmda
It attempts to also store the metadata encrypted. Admittedly got a bit carried away trying to hide mtimes.