From Dark and Darker Wiki
Armor penetration does not allow you to reduce an opponents armor past 0% and you don't benefit from having over 100%.
If you click the Armor Penetration embed in the Enchantments table just above this comment section, it will bring you to the wiki's Damage page. There you can find detailed information on how it's calculated and what it's limitations are (such as not being able to reduce damage reduction past 0%), as well as similar information of other stats if you're interested.
Cheers, Solace