alt Hacker NewsI wasn't there and have never had a security clearance. But I doubt Dick Cheney would have been satisfied with a non-functional query system during the war on terror, many years after giving direct orders to build one. Yes, I believe they were active.
I highly recommend the documentary "The United States of Secrets" by PBS Frontline, it digs into this time period and government motivations after 9/11. Usually free on Kanopy.
Star Wars was non functional. It was effective strategically (and led to the USSR's demise, partially) , but totally impotent technically.
It's just as likely that XKeyscore was a strategic public relations effort to intimidate the enemy .