This is an interesting point but I doubt any court would prevent the NSA from spying on foreign communications based on this argument.
Immigration and nationality are exclusively "guilty until proven innocent." The burden on proof is on YOU to prove that you are a US citizen, whether you're stopped by some police department or the border patrol. This is why you're supposed to always have your Green Card on your person.
In most states it is not required to have ID on you. Most US citizens do not carry proof of citizenship (passport or birth certificate), and a Drivers License is not proof of citizenship.
US citizens travel abroad, and it would be illegal for the government to intercept communications between a US citizen and someone else, regardless of location of either party, regardless of the location of the communications intercept.
Furthermore, based on your logic, the government could intercept all emails where someone's passport was not scanned and attached...
Immigration and nationality are exclusively "guilty until proven innocent." The burden on proof is on YOU to prove that you are a US citizen, whether you're stopped by some police department or the border patrol. This is why you're supposed to always have your Green Card on your person.