Couldn't this just be a coincidence? I'm sure there are many other headings whose initial letters would sum up to a phrase in some language (or otherwise transform into a message via some pattern).

Sounds a bit like the whole backmasking debacle: http://en.wikipedia.org/wiki/Backmasking

If it was real you'd think it would be a more obvious anagram, like NSA IS HERE.

So the dev encoded a very private obscure message that the NSA is inside the project, and then very publicly explains what the message is and how to read it?

I'm pretty sure it's sarcasm.

Muy latin is bad, but even google thinks the translation is off: (Like thinks it's romanian)

UTI nos im with and

"uti nsa im cu si" from Romanian

If you set the language to Latin, Translate does not complain and produces this English: "If I wish to use the NSA"

"Using TrueCrypt is not secure as it may contain unfixed security issues" sounds awkward, so looking for a coded message is not overly paranoid. But I don't think one was found. If you ask Google translate to do the reverse translation, it comes up with "Si volueris uti NSA."

Any opinions on which is the likelier Latin phrase?

These conspiracy theories are getting so ridiculous I can no longer decipher which are jokes.