I think I wouldn't want to make AMM warheads too much larger as this would significantly reduce AMM performance particularly at low tech levels while having minimal impact at higher tech levels. 0.4 MSP versus 0.25 MSP is quite extreme as it would reduce speed and thus, approximately, AMM hit rate by nearly 25%. If we scale it to the MSP required for a 1-damage warhead (which is just 1/tech level), then we can use an expression like (Size*Strength per MSP)^(3/2) which is perhaps not so intuitive for players but makes higher-damage missiles more feasible while preserving AMM capabilities.
A better way to pull back high-tech AMMs would be to reduce the missile agility gain per tech level. Currently it is something quite ridiculous: 20 per MSP, then 32, then 48, then 64... basically the early levels increase very quickly and then agility is inflated for all the tech levels. In my modded DB I have adjusted the early levels to 20, 25, 32, 40, ... in the same pattern as most numerical-valued techs in the game, and agility caps out at 250 per MSP which is not quite enough to create 100% hitrate AMMs at MaxTech without sacrificing ECCM (I think you can reach about 80-85% from a quick calculation; of course you can reach 100% without ECCM, but then ECM makes your AMMs useless). The impact is not too great at lower techs because most of the AMM hit rate comes from the engine techs until you reach the middle tiers anyways, so on balance coupled with the above change to damage it should work fairly well.