The Panau Secret Service are very rarely seen patrolling the bridges around Panau City. We have pictures of them.
And yes, there's a number of things in the JC2 files that the game doesn't make use of. These reveal several cancelled missions and locations. And some minor items. The development of JC2 is known to have been long enough that they reconsidered a number of things about the tone of the game. See the article "Cut game content from Just Cause 2".