OK, this is a HUGE change, but just a suggestion.
Current large NSF files generate two problems on Mac OS X -
a) Can’t index documents descretely with Spotlight (similar problems on Vista)
b) Time Machine (or other incremental backup tools) must backup the entire large NSF every time even though only one message changed)
These problems transcend a mailbox and apply to all databases.
Suggestion: On Mac OS X, use the bundle concept to create a file folder of individual documents.
… of course lots of other issues will crop up, but I think this would be a more modern implementation.