I am not sure I understand the initial question. Are you serious asking why you cannot "throw" the bullets harder by using your stamina? I don't understand. I know from personal training you can use your physical endurance and conditioning to hit harder at the loss of some conditioning, but in all my years of using a firearm I have never been able to use my strength to make a bullet hit harder. Since this should be obvious I must assume this is not what you mean. That brings me back to the original statement, I don't understand what you mean. If you are asking why is the increase damage skill is obtainable form range weapon leveling, I agree it is not correct and should be looked at some time in the future.
I will however agree range weapon fighting should be looked at and perhaps given an overhual.
Why doesn't increased damage work on ranged weapons?
Re: Why doesn't increased damage work on ranged weapons?
Hmm, if a double pistol wielding option was available, i wouldnt really care about the bad damage on them. Imagine flipping not one, but two! yes two!pistols more often than actually firing them at the mob 

Am i supposed to write something witty here ?