I'd hazard a guess that most proprietary formats are similar to the maildir format. Its just that the individual files are opqaue at the filesystem level. If you create thousands of tiny files then you are hoping that the file system design - which like any other design can only be optimized for specific workloads - can handle it better than a database type format specifically designed for email.
Then again a generic full text search system (which probably won't even know that they're email files) over those thousands of files would have to be better than a targeted design for email data.
You would miss certain optimizations like.. (making one up now) extracting and storing just the email headers in a separate region to speed up indexing and having some indirection built in to lookup that specific email.