Well, except that many users want full indexing of e-mails, including attachments, such that they can use an AJAX web interface to quickly search them.
So, storing all e-mails encrypted is not really feasible if you want to have such features as well [1]. It's a trade-off - convenience or security (I am sure someone will site Benjamin Franklin now ;)).
[1] Yes, I know that there is work on indexing encrypted data.