No, messages are stored in plain text using maildir format in /home/user-data/mail/mailboxes/example.com/username/.
Although not used by MiaB, encryption on a storage device is unencrypted in memory, which retains the keys entered during the boot process. Anyone at the ISP with access to the underlying storage hardware most certainly has access to the server’s memory, plus there are introduced other complexities related to how modern virtualization functions that I’m not familiar with, but as I understand it “snapshots” of a running system can be used to completely restore on different machines.
When it comes to ISPs, you are either trusting them with everything or you run your own hardware.