The three newest shelters (re)built by the AMC along the AT (Garfield Ridge, Eliza Brook, Kinsman Pond) have, luckily, been kept basically 100% graffiti free so far. Upon completion of these projects, the crews put together a journal that is kept in the shelter detailing the work and inspiration that went into building the shelters and simply ask people to not deface them. I think part of the success has been that the journals try to avoid the "but we worked so HARD on this, please don't screw it up" in favor of emphasizing that the shelters already have quite a bit of "character" already built in. Maybe wouldn't work with older shelters, but something to consider for those building new shelters or doing extensive repairs.