IIRC, the plain passwords were added because there was no better way to hand over passwords to webmail, correct me if am wrong.
same was with ftp passwords.
Why?
I have currently ispcp on one server and passwords are encrypted. (I will migrate to your panel)
I have on another server "hand made" mail server with webmail client and passwords are encrypted too.
Webmail working without problems, in both cases webmail is roundcube.
Where are you have problem with? Mabe I can help you?