[ken]

Same as any other document on my disk: it doesn't matter. Just dump everything in there and let Spotlight index it.

(That's basically what iTunes does now, except the exact behavior is hidden behind a mysterious "Keep iTunes Media folder organized" checkbox, and the index is stored in big opaque XML files rather than Spotlight.)

My email has hierarchical folders, too, but I don't know anyone who worries about the folder structure of their email. All messages are indexed, and search is quick, so there's not much point.