Here's a ground-breaking story from that illustrious news source, The Onion:
CIA Realizes It's Been Using Black Highlighters All These Years
Also unclear is why black highlighters were chosen in the first place. Some blame it on the closed, elite culture of the CIA itself. A former CIA officer speaking on the condition of anonymity said highlighting documents with black pens was a common and universal practice.
"It seemed counterintuitive, but the higher-ups didn't know what they were doing," the ex-officer said. "I was once ordered to feed documents into a copying machine in order to make backups of some very important top-secret records, but it turned out to be some sort of device that cut the paper to shreds."
That explains a lot. I suspect the FBI has made similar mistakes. I once ordered a copy of my FBI file, and received a folder full of pages with sentences blacked out. I have scanned a copy of the cover page. Perhaps you can figure out the complete content of the document. I am stumped.