Well one reason being I really like SQLite.
SQLite has a pretty great C API making it really easy to programmatically store, modify and retrieve data, which made it my first choice for runtime configuration data.
Adding another storage backend for the mail data would have meant a lot more code paths to support.
SQLite also has a lot of tools surrounding and supporting it (I particularly like SQLiteStudio) which allows querying/modifying/analyzing your mails with a huge number of programs, and using SQL - something I've found really useful!
With a sufficiently sane schema (which I hope we've achieved), transforming from the database format to any other format becomes really easy!
Also, since cmail is not really being developed with the intent to have people access their mail with a shell account (the main reason being that cmail users should not have to map to system users), supporting access formats on the server side is less of a priority - preferred access is via POP (already available) and IMAP (once it's done). The user database feature allows cmail users that ARE system users to control their own database.
An exporter to convert to/from Maildir is a planned feature :)