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Vote for this RFE:
Bug 14713 -encrypt offline messages
Based on feedback I've seen, even though you can still find/search the store folder on disk, some want
Bug 27005 - Prompt for password in offline client (for zimbra/non zimbra accounts) done earlier anyways - even without encryption behind it yet - as someone dropping by and navigating the store isn't as 'easy' as opening Zimbra Desktop.

Current best practice is to set a platform/operating system level password (at login/screensaver), OS encryption or storage/disk encryption. (Should your platform not have anything built-in you might use the open source
TrueCrypt to encrypt the entire partition for example.)