The same holds true for arrows. A broad head and armor piercing head will hit with the same energy, but the damage will be very different. Again, it has to do with how the energy is applied to the target.
Of course the old real estate adage stands true as well: Location, Location, Location. A half inch whole in the heart is bad ju-ju no matter at what velocity it was created. But that is really a side note.
Which brings me to my point that bow stats already take STR into account. Bigger more powerful bows require more STR and do more damage.
Short Bow, STR 9, 1d8
Nomad Bow, STR 11, 1d10
Long Bow, STR 13, 2d8
Dragonewt Bow, STR 17, 2d10+2 (from Monsters)
So it seems the bow stats include the STR required to use them. In the case of the Dragonewt bow an average Warrior Dragonewt has a 1d6 damage bonus and only needs to be slightly above average to have a 1d8 damage bonus on top of that. Why would they ever close to melee range?
So following the established pattern for bows a Giant Bow would look something like:
Really Big Short Bow: STR 30, 2d12+2 (and that seems low compared to the bows listed above) and the Giant still gets 2d12 in a damage bonus. Ouch.
The RAW actually work well as is for humans, but once you start getting into slightly bigger than human creatures (Dragonewts for example) they become unbalanced, and the bigger/stronger the shooter the more unbalanced they become.
I like capping the damage bonus at 1d2 or 1d4, saying that you can only push a Bow so far past it's 'normal' potential. Otherwise a Giant could still apply a 1d12 bonus to a bow that in reality would break.