I'd like to encrypt my home folder in CentOS. I notice Dovecot has created directories and files under ~/mail. If I encrypt, will my email stop working (remote access over imap and smtp)?
Your unencrypted directory is available only when you are logged in, it's a fake filesystem provided by the decryption program. When you're logged out, the fake (decrypted) filesystem does not exist.
cron cannot see it.
dovecot to only use files/dirs that exist while you're logged out.