[ndt]

"In cryptography, the objective is to keep the messages secret. The enemy's objective is to break the code and determine what the messages mean."

In this instance I think you have that backwards unless you are saying that the terrorists are trying to break into the NSA. I would like to think that the NSA has that base covered. But your general point is noted.

"This is why, for example, why we didn't use all of the intelligence that we gained from breaking the Enigma cipher - because acting on information that could only have been gained by breaking the cipher would have let the Germans know it was broken - destroying our ability to gain further information through the broken Enigma code"

Encryption today makes Enigma look like a Blue Hornet© Decoder Ring. However, in some ways it is much simpler. There is no need to arduously create a cipher every time that you need to change the code, the keys are generated automatically.

Are you suggesting that after 3 years, A.Q. has not changed changed their keys? That is absurd.

"Padilla is accused of an act of war against the US, after all - is a more appropriate venue, given the crimes alleged of Padilla."

Just curious, what do you think those crimes are?

[thoughtomator]

In this case the enemy is the code-maker and we are the code-breakers. As the code-breakers, our objectives are first to break the code and read the messages, and secondly to conceal the fact that we've broken the code, so that we can continue to read the messages, and also so that the enemy cannot take countermeasures. (Technical improvements in cryptography are reduced in effectiveness by technical improvements in code-breaking; the game remains the same.)

And so goes the give-and-take of intelligence gathering - it's all about who knows what. If we know what our enemy is saying among themselves, that's good. If the enemy finds out that we know, that's bad, because this leads the enemy to communicate truly important information by more secure means, and also this opens up opportunities for disinformation - if our enemy knows that we can snoop on one of their methods of communication, but we don't know that they know that, then they can use that method as a way of passing false information to us and having us believe it, damaging our ability to sort truth from fiction and thus to make use of intelligence in general. A civil trial with discovery in Padilla's case will reveal to the enemy some of our methods and means of spying on them - the result of which can only be positive for the enemy and negative for us.

With regards to your last question, I believe Padilla is accused of plotting to detonate a radiological weapon in the city of Chicago.

In the current situation, the code comprises all of the methods of enemy communication, not just technological ones.