Tom, are you removing the pits because you don't like seeing them? I have more than one hammer gun that has pits, on a few I have run a 400 grit hone through them and only removed .001-.0015 and left them alone. I did not take out the pits and only increased the bore by that amount.
A while back on another forum, someone wrote in about pits in their barrels and a fellow wrote in and said to go to an open field with very low grass, shoot the barrel/s that you want and watch for the wad, retrieve it and look at the wad, if it is badly wrinkled from catching on the pits as it left the barrel, then they are deep and the barrels might not clean up with honing and still be safe. This is about the best information I have heard and makes sense.
Brother Drew is pro-hone and he could explain his theory on honing. I can't, and do believe that when you hear of "mirror" bores in vintage shotguns is because they were honed out and that is why it is imperative that the wall thickness be checked. I do believe that if you clean the bores with todays solvents and I always use a bronze bristled brush so that it goes into these pitted areas and cleans them out. Also I don't believe todays primers and powders are as destructive as the primers and black powder of yesteryear.