The Vatican has one of the best intelligence operations in the world, rivaling that of Israel. With the state of our own intelligence gathering being diminished, I think they may be looking for information, not about the Vatican, but the rest of the world. We must remember that the Vatican is recognized as a sovereign state, not just a religious entity.
While I find spying on our friends deceitful, it has been done throughout history and we should not be surprised. I would also venture to guess that this has been done by other administrations as well.