I've paxed a couple of times on BA 757s with flaptrack fairings missing. On neither occasion was anything volunteered by the crew, and both times a number of passengers told cc that "something had fallen off".
Since the majority of pax will have neither the maintenance or aerodynamic knowledge to know that a missing fairing is not a problem, I would suggest that a simple announcement by the Captain before engines start would be a good idea. Standard jocular BA "Bigglese" would work quite well for this, methinks....