I like the suggestion from Bremen that each extra layer of armour reduces the percentage chance of penetration, rather than having a fixed amount that can be penetrated. For example, if the penetration rate per layer was 70%, there would be an 70% chance of penetrating one layer, 49% chance of penetrating two, 34% of penetrating three, etc.. In fact, to make mesons scale with increasing defences, there could be an extra tech line for mesons that is their chance to penetrate each armour layer. As you research more tech levels, the chance to penetrate a given thickness of armour increases. That allows you to fight more effectively against mid or late game defences using mesons but also requires a good investment into research if you want to do that. Mesons remain viable against smaller ships, or those with shield-heavy passive defences, and retain a small chance of hitting something vital on a well-armoured ship.
That sounds acceptable. The question then becomes how to carefully balance the penetration chance. And that is strongly dependent on how many armour layers the meson is facing.. I don't have a lot of experience with end-tech ships, I assume most ships will NOT go beyond 20 layers of armour.
I threw together a 1 minute thing in excel, with base chance of penetration, and how much it is likely the meson will penetrate x layers of armour.
Chance 5 armour 10 armour 15 armour 20 armour
70,00% 16,81% 2,82% 0,47% 0,08%
71,00% 18,04% 3,26% 0,59% 0,11%
72,00% 19,35% 3,74% 0,72% 0,14%
73,00% 20,73% 4,30% 0,89% 0,18%
74,00% 22,19% 4,92% 1,09% 0,24%
75,00% 23,73% 5,63% 1,34% 0,32%
76,00% 25,36% 6,43% 1,63% 0,41%
77,00% 27,07% 7,33% 1,98% 0,54%
78,00% 28,87% 8,34% 2,41% 0,69%
79,00% 30,77% 9,47% 2,91% 0,90%
80,00% 32,77% 10,74% 3,52% 1,15%
81,00% 34,87% 12,16% 4,24% 1,48%
82,00% 37,07% 13,74% 5,10% 1,89%
83,00% 39,39% 15,52% 6,11% 2,41%
84,00% 41,82% 17,49% 7,31% 3,06%
85,00% 44,37% 19,69% 8,74% 3,88%
86,00% 47,04% 22,13% 10,41% 4,90%
87,00% 49,84% 24,84% 12,38% 6,17%
88,00% 52,77% 27,85% 14,70% 7,76%
89,00% 55,84% 31,18% 17,41% 9,72%
90,00% 59,05% 34,87% 20,59% 12,16%
91,00% 62,40% 38,94% 24,30% 15,16%
92,00% 65,91% 43,44% 28,63% 18,87%
93,00% 69,57% 48,40% 33,67% 23,42%
94,00% 73,39% 53,86% 39,53% 29,01%
95,00% 77,38% 59,87% 46,33% 35,85%
96,00% 81,54% 66,48% 54,21% 44,20%
97,00% 85,87% 73,74% 63,33% 54,38%
98,00% 90,39% 81,71% 73,86% 66,76%
99,00% 95,10% 90,44% 86,01% 81,79%
I assume here that most ships will never have more than 20 layers or armour.
Based on this, I'd say that penetration chance should start at around 70% and reach 86%, with all the tech upgrades. That is quite effective against relatively low armour. And it still has 10.4% chance to penetrate 15 layers, and 4.9% chance to penetrate 20 layers of armour.
In my opinion, this is a fair tradeoff. If an enemy ship has even more than 20 layers of armour, yes it will be almost impenetrable to mesons, but on the other hand, it will have less shields and less weaponry. So... I think it's a good tradeoff.
Of course this assume that 20 layers or amour is a very high amount. If at very high tech level that ends up being sort of normal, then penetration chance could be raised. Needs balancing depending on actual numbers, once we do have them.
Edit: to further explain, keep in mind that I assumed that if you are using meson fighters, of course you have a large amount of them. That is what should be expected. So those numbers are fine because there's a lot of attacks going on every round.
And yes, you may have to escort your meson fighters with interceptor fighters to shoot down the enemy's fighters or AMMs that might attack your meson fighters. The meson fighters in this scenario operate as small " anti-capital bombers" which you have to protect