I've never seen stamps with original black paint in the lettering. Sometimes gold or silver though. When you see a heavily buffed old pipe, and the stamping looks darker than the stummel, I believe that might be from something else getting trapped in there (stain or oil) when the pipe was previously cleaned up, but I'm unsure.
I agree that you want to keep away from the stamping when you are sanding or using micromesh, but here's what has worked for me 100% of the time when I had an old overbuffed pipe with weak stamping:
If the pipe's finish is a wreck and I'm going to have to scrub the pipe clean and refinish, I will scrub with straight Murphy's Soap, using a toothbrush, then rub in Danish oil after it's dry. The stamp is often a little clearer when I'm done. The Murphy's Soap brings up the grain a little, but then the Danish Oil presses it back down (when you rub it in). Then you add whatever finish you want;e.g-carnuba wax or B&A balm, and the stamp should look even better. The key is to keep the sandpaper and micromesh away from the stamp. If the stummel is rough around the stamping I sometimes use a very, very fine micromesh and that doesn't seem to affect it, but will smooth down the 'meant to be smooth' wood around the stamping.
warning - Danish Oil will darken the wood, so keep that in mind if you're restoring a lighter-colored pipe, and perhaps find a different oil such as a Tung Oil/alcohol mixture.