I know a HBP is not counted as a walk, but in the case of a pitcher hitting a batter after already going to three balls in the count, it seems to me that the pitcher is just as deserving to have a walk counted against him as if he had thrown a fouth ball and not hit the batter. Does anyone know if there is a good reason why a HBP is not considered a walk in this case, or is it just because the rules define it accordingly.

If a pitched ball strikes a batter and he's awarded first base as a result, its a HBP, even if it would've been ball 4. The only significant difference is that the ball is dead on a HBP and live on a BB. The umpire calls the HBP and kills the play. On a BB, play on.

I will say that its sometimes hard to tell. If the pitch grazes the shirt and is caught by the catcher, unless you're watching for the umpire calling 'time out' you'll miss it.

Really not a significant difference in the result for the pitcher or hitter. There might be a slight effect on how OBP is calculated, as some include walks but not HBP in the caculation for reached base in on base percentage. I believe this is incorrect and the correct formula is:
OBP = (H + BB + HBP) / (AB + BB + HBP + SF)
from
http://www.sonsofsamhorn.net/w...ference_Page#Offense