DPS is determined by the size of the weapon, as long as you don't go over 100% slave or effect every block will add damage, 5 DPS per block. Any slave that reduces fire rate increases damage (pulse and damage beam), and any slave that increases fire rate reduces damage (cannon). Now when you start adding effects you have to consider how they affect that damage. Ion will add more shield damage but make you deal less against every block. Pierce lowers shield damage but can deal a lot more hull and system damage.