The claim that thousands of DoD employees were found to be subscribed to child pornography websites or otherwise consuming child pornography as a result of "Operation Flicker" is false. The DCIS received a list of 5,000 names of different suspects and used that list to investigate any DoD employees who appeared on that list (around 30). Among those suspects, a subset of them were found to be consuming such material. Articles are misleadingly implying that the 5,000 names are all DoD employees, but the 5,000 names are just all suspects of visiting child porn websites who may be from any background.
For additional context, the DoD employs over 2 million people when you add all military and civilian employees, and that would be pool they are searching through to cross-reference with that list of 5,000 names.