That's a good point and a good reason why it's irresponsible for these newspapers to post the details about this technology. This kind of CI doesn't work as well once everybody knows what you're doing. It also gives a road map to more oppressive governments looking for ways to spy on their citizens.
The documents do not make it clear how much of the information that can be taken from apps is routinely collected, stored or searched, nor how many users may be affected.
Right, so this is just publishing some details of NSA/GCHQ counterintelligence technology without saying how they are using it. Unless they have some evidence of wide scale deployment of these techniques, how is this surprising? Do we not expect spy agencies to develop surveillance technology?