I've yet to find graffiti anywhere on any long-haul Amtrak train. There is none in the restrooms, none in the private bedrooms, none in the parlor cars, and none in the Diner. I do spend most of my time in the Sleeping Cars which are considered First-Class and that could account for the lack of graffiti. People willing to spend at least $67 per day extra just to have a private room are probably less prone to create graffiti. It's either that or Amtrak is extremely dilligent about removing it immediately after every trip.
Local Amtrak Commuters like the San Diegans are a different story. I've already found graffiti in the restrooms of the brand new California Cars that were just placed into service in November. That is just one month after the introduction of those cars! So ... I suspect it really does have a lot to do with the type of people that ride each type of train and the lack of those people in the more expensive Amtrak accomodations.