Mail is not such a nice storage system finally...
I've come back from the experiment I did a few weeks ago, for several reasons.
- Spotlight does not index the content of attachments, so if I store a pdf in a mail message, I won't be able to find it by its content. This is a major drawback for me as I rely more and more on spotlight (along with Quicksilver).
- Mail.app does not seem to be able to deal with the amount of mails generated by newspipe (the RSS feeds to mail I mentioned a few days ago). NetNewsWire is pretty useful, and lets me very easily open interesting things in the background with OmniWeb.
So it's back to square one for this. But I make sure I have automatic backup of my Yojimbo database every night ;-).