it sounds to me, that you configured ldap as authentification module for your (courier-)imap.
sorry, i don't have any exercises done with ldap authentification for mail purposes.
pop3 relays on an existing local user (like qmail's default configuration). you might be able to add local users, but for a lot of different usertypes, this is not the best solution. as said, this is nice to me for a few handful of users.
during installation, i'd got difficulties to authenticate users on imap

. i solved this for courier, to accept crypt MD5. with adding an MD5 hash entry to every user in /etc/passwd, my users are able to logon.
but, this cannnot count as a 'tip' here, cause you have to go sure that passes are sync'ed.
but back to your question: about a year age (when i did this setup) there were possibilities for courier's pop3 to do Maildir. but this ain't a problem, because you should be free to use PAM for authentication.
(i'll check my setup in a few days to give you more information, by now, my brain is overloaded with a couple of various completely different projects...

)