That's why I pay for Evernote. Not because I really need the premium features (though I do like them), but because I want them to stick around.
So, if you're looking into long term storage and organization of your emails (and other notes) keep the future prospects of the product in mind.
Evernote does have an export feature that will let me keep my notes if the product dies. It would be very painful though, because only the notes can be exported, not all the work I spend organizing them. That's only a few seconds a note, but that adds up very quickly if you have to re-do it all.