I think the dye only penetrates a little way into the bone. Witness the members here who have sanded away some of their jigging for a pocket worn look, in the "modified traditionals" thread. In every case, the handle is significantly lighter afterwards. I myself have a Case 6375 which I think is from the 60s or 70s (I'm no Case expert, inherited it from my dad) and the bone on the mark side is dark brown with creamy spots, while the pile side jigging is much more crisp, and is uniformly black. I think the way he carried it in his pocket, the mark side received a lot more wear.
You'd expect the material to darken over time from the oil in our hands, but I think that for a knife actually carried in the pocket (as opposed to sitting on a workbench every day) the abrasion from the fabric will polish away the handle material far more than our hands will add to it.