These are meant for use on a PDF, so size is less of an issue, other than the build costs. However I also want them to be able to hit an agile target, pack a serious punch (damage 25) and be able to reach far enough to engage before the enemy can launch. To do all that, I think I need the size. If I were using missiles on ships (I'm not this game), I would make them much the sizes you suggest.
Thank you very much for help. The crucial point I was missing was to edit the stage number. I had left it at the default 0, somehow failing to recognise that flag for what it was.
I'm right now planning on launching these 100 at a time. Do you guestimate that is likely enough to saturate their defence and still have plenty left to do serious damage?
If they have a warhead of 25, then in most situations that will be enough. You will probably want to have 1 missile fire control for every 10-15 missile launchers, and to have each fire control target a different ship when firing. If you have ECM tech, you should definitely put ECM on the second stage of these missiles, they are more than large enough to fit it.
I also recommend designing two types of missiles: the missile you are currently planning, and a MIRV missile, aka a missile with the size 10 first stage and 4x size 2.5 missiles as the second stage. That way, if the enemies have enough firepower to deal with a volley of 100 missiles, you can launch effectively 400 missiles at them (Even if those 400 missiles only have a warhead of 4 or whatever).
To be fair, even 100 is more than most NPRs can deal with, I've only seen Spoiler races be able to shoot down more than 20 missiles at a time, and that was because they had a massive 283,000 ton mothership with 150 dual laser turrets. (If you ever encounter an enemy that spams FACs and their lasers deal acid damage, be very paranoid)
On the topic of final summary of stats: no, the lower hit probability is the hit probability of the first stage, not the second. It ignores the fact that its a two stage missile.
I would not bother with missile sensors. What sensors on missiles do is make it so that if the missile's original target dies, the missile will not self destruct and can use the sensor to find a new target. However, the problem is that it would require the target to die after the second stage separates, which is unlikely given how long it will take the size 20 launchers to reload. Also, missiles with sensors will all hit the same target, they won't spread out. Finally, missiles with active sensors won't keep moving after their target dies, they will stop dead in space and wait for a ship to enter their range, which means missiles with sensors are only useful if the enemy is chasing you.
Basically sensors on missiles are usually only useful for sensor buoys or as a way to remotely scout without putting any of your ships in danger.