Follow these steps to design a very simple short-range anti-ship missile.
1) Warhead Size:
Whatever size gives you a warhead value of 9.
(If you are feeling spicy, try a warhead value of 16 or 25.)
2) Total Missile Size:
Multiply the warhead size (not the value) by 3.
Round that up to the nearest valid missile launcher size (check the dropdown in the component design window), and then pick the next largest launcher size after that.
This is your total missile size.
Example:
I have a warhead size of 2.25.
Times 3 = 6.75.
That value is available as a launcher size, so I pick the next largest one (7).
My total missile size is 7.
3) Engine Power:
Select the highest power in the dropdown.
4) Engine/Fuel Size:
Calculate the difference between your total missile size and the warhead size.
This is how much MSP you have for engine and fuel.
In the engine size dropdown, select the largest size that is smaller than that.
Then change the Fuel Capacity value (on the far left) to whatever MSP you have remaining.
Example:
Total size 7 - warhead size 2.25 = 4.75 MSP left.
Largest engine size smaller than that is 4.7.
That leaves 0.05 for fuel.
5) Missile Range:
If the range is at least 2mkm, you are done.
Otherwise, drop the engine size to the next lower one available, and increase Fuel Capacity by the engine size difference.
The total missile size should be the same as before, but the speed has dropped and the range has increased.
Keep doing this until the range is at least 2mkm.
Note: 2mkm is not a magic number. It is a simple number, easy to achieve, and good enough for early defense. There are plenty of reasons to prefer having more range, or less. If you find those reasons compelling, go for it. You can still follow the above process until you have the range you want.
Another Note: If, while you are iterating the engine size as above, the fuel capacity reaches 1/3 of the engine size, stop changing the sizes. Instead, decrease engine power to reach the desired range.
6) Decoys (optional):
Decoys will improve overall effectiveness against targets with PD (point defense) weapons and/or AMMs (anti-missile missiles), but reduce effectiveness against targets without them.
If your final engine size is at least 2 MSP, add 1 decoy to the missile and reduce engine size by 0.5.
If the engine is still at least 3 MSP, you can do it again.
If the engine is still at least 4 MSP after that, you can do it yet again.
If the engine is still at least 5 MSP after that, you can do it yet again.
Note: reducing your engine size will also reduce your range, so you might opt against adding another decoy in order to preserve your desired minimum range.
Also note: if you end up reducing your engine size to less than 3 times your fuel capacity, you can likely get a better range/speed combo by increasing engine size to 3/4 of (current engine size plus fuel capacity), reducing fuel capacity to compensate, and then reducing engine power until the missile range is back to the original value (or your desired minimum range).
7) Finish the design:
If you opened the Create Research Project window (for component design) or the Ground Forces window or the Turret Design window at any time after you opened the Missile Design window, DO NOT CLICK the Create button yet.
Instead, copy your design specs (or take a screenshot), close the Missile Design window and any of those other windows that are still open, then open a new Missile Design window, enter your specs, give the missile a name, and click the Create button.
(Just trust me on this. Here there be bugs. They may have been fixed in 3.0. But they may have not.)
8) Next steps:
Design and research a Missile Launcher for this missile size.
Design and research a Missile Fire Control and an Active Sensor, each with at least as much range as this missile.
(Instructions for these steps are beyond the scope of this guide.)
I posted a version of the above on Discord about a year ago.
Criticism and suggestions are welcome, here or on Discord (where I am available and responsive a worryingly large percentage of the time).