projectile damage is (usually) defined in the datablock of a projectile, so it cannot be directly modified in-game
HOWEVER
You can hook into armor::damage and make sure you are hitting a bot, then check to see if the projectile is a certain damageType and reduce or increase the %damage as needed
Here would be a quick example script
function Armor::Damage(%this, %obj, %sourceObject, %position, %damage, %damageType)
{
    Parent::Damage(%this, %obj, %sourceObject, %position, %damage, %damageType);
    //Make sure we are hitting a bot
    if(%obj.getClassName() $= "AIPlayer")
    {
        //Default sword does double damage
        if(%damageType $= "Sword")
        {
               %damage *= 2;
        }
    }
}
there are other ways to achieve the same effect such as using projectile::damage as phantos suggested