Well I'd like to avoid this debate if possible. It really comes down to whether you trust a business or the government, and there are arguments for one over the other and for neither.
But no matter what, the email is going to go through someplace - we don't have a choice about that - and one of the clearest points to come out of everything we've learned is that your ISP is probably the weakest link in the chain for all of this stuff.
Basically I'm saying that it's foolish to think that just because you're hosting your own email server you're safe from the prying eyes of the NSA. It doesn't matter.
So yes, having your files on a server would make them less easily seen by the government. But then you're more susceptible to the other drawbacks of local storage.
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Matt