We all used to mark case heads on pistol brass with Magic Markers in the bull's-eye league. There were lots of funny ink stripes and quarter pie slice color patterns and the like to identify our pickups as our own. One day, though, I noticed the breech face of the slide on my Goldcup was getting tacky. It was a build-up of the ink. It took some solvent to get it all off. It didn't hurt anything, but I'm just mentioning it for awareness purposes and to suggest that if enough got into a firing pin tunnel from inked primers, it might cause erratic lock time or weak strikes.
If you are marking the brass for load identification rather than case identification during brass policing, you might consider using colored Sharpie markers just to put bands on your bullet ogives. It won't affect the bullet ballistics, and the ink is gone and out of the gun after firing, rather than becoming a cleaning problem, though I suppose a feed ramp might eventually need a wipe. Indeed, you could use the resistor digit color code to put the charge weight on each bullet by assuming a decimal point before the least significant digit. Read from nose toward base so you can remember the band that is highest when the cartridge sits upright is the most significant digit.
0 Black
1 Brown
2 Red
3 Orange
4 Yellow
5 Green
6 Blue
7 Violet
8 Gray (this is the only troublemaker for marking a bullet, so use a silver Sharpie)
9 White
Yellow Red Green = 43.5 grains
Orange White = 3.9 grains
et cetera.