Those are good questions.
When I have seen a Gunnery skill use Smarts instead of Agility it has been in the case of a different type of firing method. What I mean is that a direct-fire weapon, like a bow or a firearm, it uses Agility. Indirect methods include mortars and other artillery. Another method is like from a starship where the targeting is made with calculations of distance and location. The gunner does not aim the weapon like at a turret, but by sitting at a computer display and is assumed to enter data and select when to fire. These cases would be Smarts, where coordination is not as of a factor as using your brains.
As for a weapon using Smarts, there are two things to consider. The ranged weapons on the character sheet are all direct fire weapons, and would use Agility. The Ranged Weapons, like you have noticed, is hard-coded to use Agility with no obvious and easy way to make it use another attribute or skill (hence your post).
What I am getting at is that many weapons that would use Smarts are not on the character sheet (starship mounted weapon), but some can be carried around (like a mortar).
Interestingly enough, Hero Lab makes an error. It gives a Shooting value for an attack with a Claymore. Really? A character makes a shooting roll? No, that is an error, and what SHOULD be the case is to have a field in the Special Weapons to select a skill or attribute or just turn off that "Attack" value.
