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Since this popped up let me add my voice to all the concerns you pose about cloud computing.

I am in control of the other apps that sync with my handhelds and I too was a Yojimbo user and synching Yojimbo to my Palm before I moved to an iPod Touch. Now I too use Evernote but I am not happy about it.

There are issues with Evernotes encryption ( which I use but it's a kludge to get ti to work properly) that make is unreliable.

Currently passwords and stuff are stored in 1Password, which syncs wifi over my own personal network.

If you ever find another app that supports notes like Evernote or Yojimbo that syncs over Bonjour or local wifi only let me know as well.