I think the basic flaw here is that author assumes that NSA does data-mining. I personally doubt it.

Rather (and here I'm going off on pure speculation myself) I think they can use the system to start with some off-line lead (say one of the Chechen bomber brothers) - and see who he was calling / emailing and then checking if there is anything valuable there.

Ie - how in the past FBI would do an investigation off-line and talk to people and piece things together - they are looking to be able to replicate it (possibly by going back in time) online.