Mmhmm, both can penetrate shields.
I think K.O. Punch just outright negates shields while the custom Jolt Haymaker bypasses shields. They don't break shields like Marth's/Lucina's Shield Breaker.
So, Marth's/Lucina's Shield Breaker, well, breaks shields.
Little Mac's K.O. Punch negates shields.
Little Mac's second custom Jolt Haymaker, Guard Break, bypasses shields. I don't know if it damages shields, but I know it ignores shields to deal damage. The name is misleading since it doesn't break guards/shields at all. It should have been called a Precision Haymaker, Guard Loop, or something that implies it bypasses shields instead of implying that it breaks shields.
Ganondorf's Dark Dive and Flame Choke; Captain Falcon's Falcon Dive, Yoshi's Egg Lay, Kirby's Inhale?, King Dedede's Inhale?, and Bowser's Koopa Klaw ignores shields since they're all grabs. Generally, in fighting games, grabs will ignore shields. It makes sense since you can counter, parry, and block hits, but you can only counter and parry grabs since if you guard against a grab, then you're a sitting duck.
Also, most Final Smashes negate shields like Ike's Great Aether, (Toon) Link's Triforce Slash, Zelda's/Shiek's Light Arrow, etc. I think there are some Final Smashes you can shield against, but you're probably going to have to perfect shield since, say, Wario Man, will be doing a ton of damage that can probably destroy or almost destroy a shield.