I would imagine that these examples could have been individually captured, traded for or even battlefield pickups. I'm really not sure that you'll be able to find a primary source stating "Today we captured two boxes of Colt's pocket revolvers" or anything to that effect. The 1849 Pocket would not have been an issue item, unless I'm completely wrong. I have no doubts that Confederates would have and did get their hands on quite a few that were made well after the start of the War, but this would have been from mostly small events.
Of course, we do know that New York was shipping more goods into Matamoros to trade for Confederate cotton than England was, so it is entirely possible that pocket pistols could have been on one of those boats. As the 1849 is .31 caliber, and the Yankees seem to have been trying to issue .36 and .44 weapons, I really don't think there would have been large enough quantities in one place for the Confederates to capture.