I just checked and penetration damage was never a vanilla damage type, this is added by Bob's Warfare. Despite this, Bob's warfare is now mostly compatible with KS Combat and you should find that the penetration damage is there for AP magazines when using Bob's. Also, the scatter cannon shell is now working correctly with Bob's, using Bob's default graphics for it. The one thing I was not able to easily fix was penetration damage to piercing shotgun shells, it just was not very easy to implement and I don't want to accidentally break something else by tinkering. Just pushed this update to live, let me know if there are any other issues :)