4 slots: 1 dual laser, 1 MKIII, 1 artemis missile, 1 minibeam - 12 damage volleys, 1.4dps after first strike, 8 power
4 slots: 4 MKII - 12 damage volleys, 1.1dps after first strike, 8 power
Clearly superior, even before considering the following:
For most (of my, anyway) ship builds, I generally have missile or bomb slots that I only fire once or twice. These are "as needed" weapon. They take up a slot, either way, but they do their job and don't really add to DPS as a primary goal. As example: My ion bombs. I'll often only fire these once per battle, at the beginning. They only take 1 power. But I really couldn't do with them. Then I might have a glaive beam, and then a breach missile, and then my burst laser.
All big ticket items, sure, but I don't need them all active at the same time, and versatility is a wonderful thing. Ion bomb, MKIII and Glaive beam to start is a nasty combo, especially with the pre-igniter, and is something I've gotten a few times. I could get a point more damage out of 2 MKII, but then I'd lose my utility slot - a breach missile for suppression of enemy drone rooms if my volley can't get through to do enough damage, a bio beam or fire beam for killing the enemy without destroying the ship once I've beat it down, a healing burst to keep my guys alive in an emergency. (easy enough to switch from ion, which I really only need for the opener) Or even a dual laser to switch to and pile on a bit more damage after the ion does it's work.
And a number of ships do only have 3 weapons, yeah. But even on the four weapon ships, gaining an extra point of damage doesn't seem worth giving up a weapon slot and the versatility it offers.