Hi! Sorry for the late response. I personally only knew a small fraction of the information about Taijutsu/Ninjutsu Pen and asked for a better clarification. It is a difficult concept to grasp but I will try my best to explain what they do.

Pen. does not affect normal damage, it affects Critical. What that means is that the more Pen you have, the more damage that type of critical will do. Taijutsu Pen corresponds with Defense, while Ninjutsu Pen corresponds with Resistance. Due to Defense and Resistance, there is a cap to the amount of damage a Critical can do. By increasing the amount of Pen you have, you increase the cap to the amount of damage you can do, which effectively increases your damage.

TLDR: More Pen = More Critical Burst

Note: This information is courtesy of Tobei, hope it helps!

~Jib