If you’re in Linux, you can use eCryptfs to setup a private encrypted directory, move the ~/.thunderbird directory into it and just leave a symlink to it in your unencrypted home directory. Then you can store your emails in plain text in the encrypted private directory.
It’s not even complicated to set up: most Linux distributions are setup so that the private directory is automounted upon login: when you’re not logged in, your data at rest is encrypted. It only becomes readable when you’re logged in.
Both my Thunderbird and Firefox directories are stored in my private directory.