I am not sure of the answer of whether they graphited smoke boxes in the 19th century. However, having used black on the smoke box and stack on Eureka, I can tell you this. Black paint (high temperature) lasts only a few years and then you have to re do the whole damn thing by removing all the old paint, priming the surfaces and painting it all over again. Black looks great, but it is the one maintenance thing I do not look forward to doing.
Back on the 125th anniversary of the Golden Spike, Bob Dowty asked several of us Nevada boys to come over and help him get the Jupiter and 119 ready for the event. My job was to graphite the 119 smoke box. It was a bit messy but a lot easier than stripping off paint and repainting. So, I guess as soon as some mechanic found this out back in the day, he threw his paint brush away and started slopping on graphite.
Dan