So, I had wondered if the penetration of a weapon increased the chance of the "Shock. My initial thought is "no", but then the shock quality seems underpowered. Also, it makes sense to me that pentration should help since it is effectively punching through armor.

What do you guys think?

well i may be mistaken but as i recall there is nothing as per RAW stating penetration helps other than just cutting through the armor itself. in fact however there is the contrary stating that for every point of armor that damage is going against the toughness test is made easier by 10% so for 3 points of armor then it would be a easy +30 toughness test. so yes shock is underpowered especially against heavily armored opponent but think of it this way. when you are putting down a riot and you break out the shock mauls you're not hitting the person you're hitting the armor they're wearing and not in contact. so against an unarmored rioter then its quite effective. then again the magic phrase is as always "ask your GM" you may be able to house rule it in favor of penetration makes it a degree harder on the test when against armor.

what i would go with is for each degree of penetration, it cancels one armor point towards toughness test.

I do not see why a Mono Officer Cutlass(pen2) against a hardened bodysuit(av3), would not have Shock effect at T+10% instead of T+30%. Yes, Shock is much better against unarmored targets. It's a matter of crowd/mob suppression versus putting down a comparative opponent.