Punch-Through, Pierce, and Ion got replaced by a new damage types thing involving Heat, EM, and Kinetic damage types.
Heat, primarily on Missiles, melts armor.
EM, primarily on beams, fries shields.
Kinetic, primarily on cannons, shreds system blocks.
The three damage types each have effect computers and modules to let you change the damage type composition of your weapon towards favoring the type connected.
You'll probably be looking for the Heat computers and modules to replicate the old punch-through.