The Russians built hundreds of 200 ton missile boats that carried 4 Tomahawk-sized missiles. Just as even a fighter in Aurora can carry all but ludicrous-size missiles. There is no correlation between per-missile damage potential and ship size.
Aurora does have hit locations, it has armor columns. You concede that high damage weapons can stack hits and end fights faster but you somehow still conclude that 'damage is damage' ? :/ The fewer stacked hits you require to penetrate the armor and start inflicting internal damage, the less total damage you have to do to a vessel to kill or mission kill it.
In any case. The damage model is not irrelevant, but it misses the point. The size 1 problem is as follows: you can have a group of warships which can stop or mostly stop a wave of 50 size 4 missiles, but they will still be hit by 150 of 200 size 1 missiles. There is no active defense strategy that will help you against size 1 spam without overwhelming superiority in BP or technology. All you can do is stack on armor or stay out of range. Non-ablative armor would not fix this problem, since it's still possible to swamp defenses with size1s.. You can even put stronger warheads on small missiles. (Say hello to uncle MIRV.)
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FWIW a Size1 AMM is about the size of a Tomahawk or the Russian Styx. With a nuclear(or better) warhead. These are big booms you are suggesting having bounce off!
It is at the end of the day not relevant if 4 missiles can do the job of 40 missiles if it is easier, cheaper and simplier over all to achieve 40 missile salvos. Which under aurora's system it is. Box launcher, FACs, size 1 launchers etc. That it is easier to stop the 4 missiles is just icing on the cake. With Aurora's armour locations once I scrub off 50% of the amour from one row, I start working on the next, with 40 missiles I am going to bore deep holes anyway just from random chance, but you require random chance to get fast penetration with bigger warhead missiles anyway. If the armour is deeper then their penetration then the 4 larger missiles are more likely to make 4 holes in the outer layers than stack on each other. I could do the math to see if the chance is higher for 40 missiles to punch through than for 4 missiles but it still comes down to luck.
Where we are going around in circles is that we haven't defined what we want to achieve. If I want to kill the ship and that is all, then I can say it has so much internal damage capacity and so much armour and I have to do that much in the way of damage to the ship. So the ship has 40 internal hits and 100 armour hits and it takes 140 damage to destroy it. How I give that 140 damage is in the first pass not relevant to the price of tea in china. If I say I want to destroy the ship as fast as possible or with as few hits as possible then the way the damage is done matters. To be clear I am talking about the first situation. So to me it is the case that 1 pt of damage from a warhead of 1 is the same as 1 pt of damage from a warhead of 9.
To be additionally clear the use of damage patterns makes weapons distinct and adds flavour but otherwise it is still ablative armour. The inclusion of armour locations in my view doesn't change the issue with ablative armour, it just makes for more tactics in the game itself. At the end of the day enough small weapon impacts in the same armour area are equal to a single large weapon. In most games this leads to the swarm.
In aurora you have two problems: the first is that it easy with size 1 missiles to overwhelm any sensible missile defence, and the second is that the missiles are capable of inflicting damage to the ship or ships targetted.
The first problem is due to the many things. Point defence ranges are also so short that you can't thin the salvo out in the time you have (due to absurdly high missile velocities). As the salvo size is larger than typical counter missile salvos you probably can't stop enough missiles with your area defence ship and have to rely on point defence fire and in which case see above. Those are things to do with the mechanics of aurora, and could be fixed in a variety of ways.
The basic problem though is that the size 1 missile is capable of inflicting damage on the ship. Because if it wasn't then you would not be firing the 150-200 missile salvo in the first place. And it is capable of doing that damage because the armour is ablative. I am seriously dubious people have a size 1 missile with a warhead that does 4pts of damage, they almost always will keep the warhead damage at 1 and use the free space for more range, more speed and more manueverability. But if I wrong so be it, but I have been assuming right from the onset here that people are complaining essentially about getting hit by large numbers of Anti-missile missiles with size 1 warheads used in an anti-shipping role.
If you want to fix the missile damage problem then you have to do something about the root cause rather than treating the symptoms as far as I am concerned. If a size 1 warhead had no chance to damage a ship, there would be no 150-200 missile salvos*, and there would be no problem to solve. In real life you can fire a SAM at another ship, but the damage to the other ship is not exactly overwhelming. Much the same way as firing 20 mm AA guns would do "something" but rather a lot less than 12" main guns to use a WW2 example.
*Or at the very least the missiles would be less accurate, slower and shorter ranged which gives you a better chance of stopping them as a larger warhead on a size one missile has a significant performance impact.