General comment (yes I know I am coming from the Canadian viewpoint, which is understandable since I am Canadian) - despite all the rhetoric about long guns, I think the big difference between overall American and Canadian gun mortality rates is the presence/absence (well rarity of legal) of handguns. Sure long guns are more useful if you are about to commit a massacre (or want to shoot someone from a distance) - but the total mortality difference is most likely due to handguns.
You are completely, absolutely, correct. Rifles accounted for 400-ish murders according the FBI. That leaves over 12,000 murders committed by other weapons, handguns being far and away the majority.
And although I can see a military use for handguns, it is minor - are they truly covered by the amendment?
According to the Supreme Court of the United States, firearms are a 'right' of the individual, for the purpose of self-defense, if a person so chooses. Handguns are a premier form of self defense firearm, so it would seem they are covered.
A slight adjustment to that ruling. SCOTUS ruled that a state can regulate or ban a firearm if it does not serve a use in a "militia". That is why sawed off shotguns tend to be banned or severely restricted. They serve not useful purpose in combat.
This. Handguns are still carried by officers & NCO's in non-combat roles, which is why they are protected by the 2nd. The part about their usefulness in a military context is the determining factor for protection from state level restrictions. However, the ban on short barreled shotguns & rifles could now be challenged. First off, it is widely recognized that the SCOTUS ruling that upheld the National Firearms Act limitations on short barreled shotguns was poorly argued, and likely would have gone the other way otherwise. Also, these days both these types of firearms do have a military purpose. The short barreled rifle is widely used today, because of bull-pup designs that allow the bullet to reach effective velocities in a shorter overall weapon, while proving more practical in close order combat situations, such as "house to house", allowing the user to swing the business end around faster as they turn a corner or enter a room. The short barreled shotgun has use as a "breaching weapon", basically a special shotgun shell is used to blow the lock off of a door suddenly just before soldiers storm the building. Swat teams use this on a regular basis for "no knock" raids domestically as well. However, a "pen gun" has no military use that I know of, and those are restricted at the state level in almost every state, I believe. Also, a weapon that is often called a "bang stick" (not the slang term for a long gun), it's a pole with a plunger trigger on the other end from the handle. It is used by divers to defend themselves from large, dangerous creatures, such as sharks. They are not restricted in coastal states, because of their obvious usefulness, but they still require a class 2 tax stamp. They can still kill up close, obviously, so they might be banned in places such as NYC, I'm not sure.