I think there a couple of considerations for missile damage beyond the pure theory which are missing here.
First, even though perfect squares are ideal for armor penetration, their importance is somewhat less if their armor penetration is not as great as the number of armor layers on a target. A 9-damage missile hitting a ship with 4 layers of armor is not going to penetrate on the first hit anyways, and in that case the distinction between, say, 7/8/9-damage warheads gets closer to linear - the exact details I'm unsure of and someone with more math or a program at hand can give more details, but generally the more armor the enemy has the less hitting a penetration breakpoint matters. This is especially the case if an enemy uses shields, as in this case you just need the most possible damage delivered to the target to break their shields.
On the flip side, hitting a breakpoint is not always critical compared to getting the desired speed, range, or accuracy on a missile. If you're making a size 6 missile, you might want to choose between a 9-damage "optimized" warhead versus a 6-damage warhead that offers more MSP for engine, fuel, etc. in order to deliver that damage to the target more reliably. Particularly if you have some good intel about the enemy's AMM and PD capabilities, you can determine the expected damage per missile and may find the warhead with less damage has a better overall effect. Similarly you might find at your tech level that you can fit 10 or 12 damage onto the same missile for a reduction in speed, but a net increase in damage if your enemies have poor PD - say they have bad propulsion but a lot of armor and shields.
As for the actual suggestions: the first one doesn't actually solve the breakpoint problem, it just shifts the optimal warhead size based on the %chance to absorb the damage - really all this accomplishes is a nerf to missiles which is just not needed - box launchers are the problem, not warhead damage profiles. For the second one I can't see a lot of use from it, aside from JP assaults I think most players prefer to use their ship tonnage to mount useful modules - first maximizing weapons and propulsion, then preferring armor and shields to prevent internal damage entirely rather than an extra module that only plays with probabilities and takes up valuable space to do so. Ultimately, with both of these suggestions I don't see any change over what we already see shields are used for, and as shields already exist there's not a lot of reason to duplicate the functionality for all practical purposes.