Is it normal to have pins in the cup of "cup and cone"?
Thank you for the clearer photos.  From them we can clearly see that the pinheads are not in the way of the bearings as they roll around the bearing surface.

To test that, grab a single bearing and put it in the race so the visible wear band is straight down.  (ie hold the hub at an angle)
Then use your finger to roll the bearing back and forth around where the pinheads are, but stay on the visible wear track.  If you feel the lumps as the bearing rolls over, then I'm wrong and they ARE interfering.  If not, they aren't interfering.

Note I'd choose to run bare ball bearings in this hub, not a pre-assembled bearing cage.

If the marks really bug you, consider using a Dremel or some super small tool to buzz off the lump.  You might be able to scratch them off with a flat screwdriver.  Would be very hard to get a file onto that surface.   Clean the bearing surface well to remove all metal dust once you're finished.