Yeah, this is an excellent point. For the Inky product mentioned in the article, a good explanation of how they handle key storage and distribution is provided here: https://medium.com/ink-different/how-inky-stores-encryption-...
30 karma · joined December 28, 2012
As for the cloud sync, we do so in a completely secure way. Our employees cannot access your accounts or read your mail. See http://inky.com/faq/how-does-inky-store-my-passwords-and-oth... and http://inky.com/faq for more details.
If you're looking for a usable IMAP/POP mail client today, try Inky (http://inky.com), which has a lot of these features already and many more on the roadmap. It's available for Mac and Windows right now, with Linux support coming soon (http://www.omgubuntu.co.uk/2013/05/inky-pens-linux-support-o...)