Mythbusters proved repeatedly that most firearm projectiles cannot penetrate more than 18" of water, and that their effectiveness was seriously diminished within just a few inches, and that the higher the power, the less effective it is shooting into the water. They expend most of their energy when breaking the water surface tension. A .22 did a little better than some, but not much. The best at shooting into water was a .50 muzzle loader. It penetrated the water by 3 or 4 feet before completely expending it's energy. They were shooting at a piece of Plexiglas under the water in a swimming pool. Water creates a lot of drag on the bullet. Sometimes enough to fragment the projectile on impact. Also, the more perpendicular to the plane of the water, the greater the effects of drag. Less of an angle increases the chance of a ricochet.
I think the reason the blowgun would actually work is the same reason that a bow and arrow works. Less drag on the projectile, and extra kinetic energy from the length of the shaft. The shaft keeps pushing the projectile forwards until the energy in the end of the shaft has been expended.
Just my .02. Also, I shot a pigeon once right in the head. It flew off with a, orange ball attatched to it's face.

oooh: Guess I used the wrong dart.