The Armed Guard officer's reports are entirely different from the various other logs you mention, although there would likely be some overlap of information.
The smooth log, captain's log and other logs (deck log, engine room log) would all be maintained by the civilian merchant marine crew. As such these logs would concentrate on the merchant marine crew and the operation of the vessel.
By contrast the Armed Guard officer's reports would focus on the Armed Guard crew, its activities, and any events involving the defense of the ship. Any actual or potential attack would certainly be noted. So it is possible that events not recorded in the various merchant marine logs might appear in the Armed Guard officer's reports (and vice versa). The quality and detail found in the Armed Guard officer's reports varied depending on the diligence of the officer in command, but it is entirely possible that you would find information in the reports that may not be mentioned in the other logs.