Be fair, there's NO video game (to my very best knowledge) that doesn't do this. It even has a nickname, "topping off the mag".
Spoiler Adam Lanza, the shooter at the Sandy Hook Elementary School, was said in some reports to have switched magazines halfway through in this style, thus adding fuel to the fire for those who want to blame games for violent behavior.
I suspect the real issue is that it would add incredible amounts of complexity for the game engine to track how much ammo you have in your current mag, how much you have total, and then how much you have in each of your magazines as well; especially in a multiplayer like Destiny or Call of Duty. Add to this that it would have to track how many mags you have for each weapon as well, and (in Fallout) take account of mags for multiple weapons of the same caliber... I'm sure it could be done, but how many players want that level of realism?