I think that is an excellent point, and along with that, comes the rate of fire component as well.
At reload 4, your size 1 launchers are running at 10 seconds per volley. Size 4 launchers are running at 30. So, the ship with size one launchers is running 6 salvos to the 2 salvos from the size 4 ship. Assuming similar warhead sizes and range, the damage ratio is clearly in the favor of the smaller launchers. As the reload rate comes up, their is a noticeable shift in the favor of the larger missiles.
(For illustrations sake, this is using the following for baselines. Cobalt warheads (10pts) and Magnetic Confinement drive tech, compressed carbon armor. Range is identical, speeds are identical, hit chance is identical.)
Size 1 missile
Missile Size: 1 MSP (0.05 HS) Warhead: 4 Armour: 0 Manoeuvre Rating: 20
Speed: 31200 km/s Endurance: 34 minutes Range: 64.2m km
Cost Per Missile: 1.7708
Chance to Hit: 1k km/s 624% 3k km/s 200% 5k km/s 124.8% 10k km/s 62.4%
Materials Required: 1x Tritanium 0.5208x Gallicite Fuel x625
Size 4 missile
Missile Size: 4 MSP (0.2 HS) Warhead: 12 Armour: 0.2 Manoeuvre Rating: 20
Speed: 31200 km/s Endurance: 34 minutes Range: 64.2m km
Active Sensor Strength: 0.28 Sensitivity Modifier: 140%
Resolution: 30 Maximum Range vs 1500 ton object (or larger): 210,000 km
Cost Per Missile: 5.6633
Chance to Hit: 1k km/s 624% 3k km/s 200% 5k km/s 124.8% 10k km/s 62.4%
Materials Required: 3.05x Tritanium 0.28x Uridium 2.8333x Gallicite Fuel x2500
At reload 6, the size 1 launchers drop to 5 seconds, for 12 salvos a minute. With a damage of 4, thats 48 pts of damage output per launcher.
At reload 6 the size 4 launchers drop to 20 seconds, for 3 salvos a minute. With a damage of 12, thats 36 pts of damage per launcher.
At reload 8 the size 1 launchers are still 5 seconds, for 12 salvos a minute. With a damage of 4, thats 48 pts of damage output per launcher.
At reload 8 the size 1 launchers are now 15 seconds, for 4 salvos a minute. With a damage of 12, thats 48 pts of damage per launcher.
So, at Reload 8, from a total damage perspective, the missile sizes are a wash. The advantages of the smaller missiles are still there (numbers) and with the hit % being identical, the chances are that the smaller missiles are still going to get things through to do damage.
As the tech goes up, missile intercepts go up as well as anti-missile defenses improve, more missiles are intercepted. This would argue strongly for the numbers approach with more numerous but smaller missiles.
Arguably though, the larger missiles are becoming MORE capable as the tech goes up. In the size 4 design above, the missile includes some armor and sensors, which the size 1 lacks. In the case of the size 4, its relatively easy to modify the missile further to improve survival, or speed, or range while maintaining the same warhead yield. Thats not possible with the size 1 missile. The larger missile also has improved penetration vs. the size 1.
So, the question at middle and later tech is smaller + numbers vs. larger + damage/penetration/flexibility.
I think that the smaller missiles have a significant number of advantages, especially so early in the game. In fact, they are probably game breakingly advantageous early on. By middle tech levels, there are some advantages to the bigger missiles that start to become apparent. In terms of flexibility, the advantage goes to the bigger missiles, since its easier to modify the fuel/speed parameters of the design without losing damage. This flexibility is ESPECIALLY pronounced if sensors/ecm are part of the mixture.