You can only fire one missile from a Launcher at once, so, no, a Size 4 Box launcher can fire only one size 1 missle, not 4.
Missiles are a system reliant and a variety of various techs, and they'll become much more capable with higher tech levels.
As for the Warhead strength, keep in mind the penetration.
The Crater of a Missile is always shaped like a Pyramid, so the root of your warhead strength is how many layers you can penetrate with a single hit.
So, WH 4 penetrates 2 layers, WH 9 penetrates 3, WH 16 penetrates 4, and so on, it's always squares.
But WH 6 will penetrate 2 layers as well, and WH 15 will penetrate 3 layers.
This is of course only important if you intend to quickly strike down a target.
If the enemy has 20 levels or Armor and you want to sandpaper it, everything above Strength 4 will generally prove to be useful over time.