Firstly, Bonebreaker and it's identical perk in the Two Handed tree are rather useless, but not for the reasons you think.
You see, armored enemies have no actual armor skill and their armors are always unimproved, so even a bad guy decked out in Deadric armor with a shield is only barely going to have over 100 points of armor rating, if that at all. By the time you can get all three ranks in the perk (requires 90 skill), you'll be dealing enough damage with the weapons you'll have by then that enemy armor rating makes little difference.
This remains to be confirmed hovewer; enemies do have classes with different skill multipliers, but how the multipliers affect their skills is unknown so far. For example, in the formula for calculating armor, NPCs have a much higher multiplier for skill level than players, so it
might be that they do actually have armor skill.
Althrough even if the hypothetical 100 AR enemy had 100 Heavy Armor skill, it would increase his AR to only 240, which means only 28.8% damage reduction. With 3/3 Bonebreaker, you would cut that by 3/4, to 7.2%. So yeah, you'd be doing ~20% more damage than other weapons, but then again how many enemies clad full in Daedric Armor and with 100 Heavy Armor skill are there in the game?
tl;dr: yep, it's pretty much worthless, just like all the weapon-specific skills.