All FPS's I know of return unused ammo in a removed magazine back to the users overall ammo count.
For example, I have 3 magazines with 30 rounds in each, I fire off 25 rounds and do a magazine change. I do this another 2 times so i technically have 3 magazines with 5 rounds in each, but when i reload I have a magazine with 15 rounds, somehow they have all jumped into the one magazine.
Yes, I am overthinking it and it probably wouldn't be fun. I'm just trying to narrow down the reasoning, especially games like modern warfare 2 which in terms of weapons are pretty much accurate in every other regard.