The Talent Hammer Blow says that one can make an All-Out-Attack with additional Armor Penetration equal to 1/2 a character's STR bonus, as well as adding Shocking to the weapon quality.

Shocking states that if a target takes damage from the shocking weapon, it must make a Toughness check +10 per Armor Point on the part of the body that was hit, or be stunned for some number of rounds.

My question is, since most creatures are much tougher in Deathwatch than DH, most creatures would have over 100% chance to make this check, which for me raised the question: does Armor Penetration from the attack (including that granted from Hammer Blow) prevent the target hit from gaining the +10 bonus for that amount of Armor on the part of the body that was hit from the attack?

Most of them have Unnatural Toughness, which increases the Toughness Bonus, not all of Toughness. A Toughness 45 creature with Unnatural Toughness (x2) would have a TB of 8, but for Toughness tests (as Shocking calls for) would still need to roll 45 or under not to get stunned.

In addition to this, I would read that rule as +10 per AP that applies to the hit, so yes, if your Pen beat the armour, the opponent wouldn't get any modifiers.

So yea, if you are hitting hard enough, with something sharp enough, you should be fine stunning things.