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On many of the modern Unix variants, /etc/passwd is only a textual representation of a database file which holds the real user information.
getpw*(3) uses this database file to access passwd data. This makes things way faster than it used to be, for example, on SunOS4, where ls(1) was written so stupidly that it scanned the (sequential) passwd file for every single uid lookup it needed to make. Typing "ls -l /home" on a SunOS system with like a thousand registered users was an invitation to get ahold of some (some!) coffee.

Speaking of today, FreeBSD uses a DB database to store passwd information (in fact, it has two databases, one with and one without passwords, for "security"). This speeds up lookups quite a lot, but beware: The DB files are still generated text files, so adding users with such huge user databases is a real pain.

The question is whether you actually want to create that many Unix user accounts. For mail servers, you can often get away better with creating mail accounts only. This requires some hackery with your friendly MTA (postfix, qmail, sendmail, exim or even smail), but it is quite doable and also has positive security side-effects.

Look into Cyrus imapd you need message store implementation which is able to handle mailboxes for users who don't have a unix login. Beware, Cyrus comes with a pretty tcl-based administration interface which you almost certainly want to replace by a bunch of home-grown perl scripts to automate administration.