Since I was curious how I could better optimize my missiles, I ran some more numbers. I didn't fully optimize everything, and only really ran the numbers using the tech I currently use. So this is not perfect information. But observations I made that seem like they may be generally applicable:
Size 1 missiles with a single strength 1 warhead are okay against both ships and other missiles, but not amazing against either. I think the best use of them is probably as an anti-fighter weapon, but I haven't really looked into this.
Assuming full size launchers and equal amounts of tonnage devoted to missile launchers and PD, and no ECM, size 1 missiles will result in the highest DPS. They will, however, apply this rather inefficiently. Depending upon the variables, they may have the highest damage per volley, but much of it will be wasted on armor compared to missiles with bigger warheads.
Assuming full size launchers and equal amounts of tonnage devoted to missile launchers and PD, there is a fairly reasonable chance that at least one missile from every volley will make it through, at least with the variables that I was using. Obviously the variables will differ wildly based on the encounter.
In most situations, if the enemy has halfway effective PD, you really want to use reduced size launchers. In one case, it turned an average of 1 hit per volley into an average on 9 hits per volley, using . 3 size launchers.
Overall, midsized missiles in reduced size launchers seem to be most effective, though there are other good options. Each situation will be different, of course.
Beam PD, shield regeneration, tracking time bonus and ship decoys are all as or more effective against AShMs than they are against AMMs. This much is undeniable.
I'm not sure that ship decoys are actually more effective, though. I think it's the other way around, actually: ships decoys are less effective against missiles that have ECCM, which typically means larger missiles. Smaller missiles are probably more likely to trigger ship decoys to deploy, since a greater total MSP of them is likely to get past PD, but bigger missiles do more damage per MSP typically (so not as much needs to leak to be dangerous). This does mean that small missiles will go through ship decoys much quicker, but the decoys will (I think) be more effective per tonnage against the small missiles than against the larger missiles.
Beam PD will not stop as large a percentage of small missiles as it will larger missiles. The entire point of using size 1 missiles against ships is to saturate PD. But to remain somewhat effective against other missiles these small missiles have to make compromises that mean they aren't as effective against ships as they could be, allowing your other defenses to make them much less of a threat. ECM in particular will be very effective, but they will also be rendered far less effective with armor.
And I also contest that AMMs *are* more dangerous, because while failing to intercept AShMs has worse consequences, it's also easier. Even if only 20 AMMs got through every 10 seconds, that's still ~600 damage if you were attempting to close 2 mil km with a 6000km/s speed advantage.
They could probably actually use that space much more efficiently with larger missiles using reduced size launchers and far fewer reloads. It wouldn't be hard to have the same volley size, doing much more damage in total, except in infrequent spikes, by using dedicated ASMs in reduced size launchers.
So, yes, it sounds like in this situation, the size 1 missiles are more dangerous, simply because they are overusing them. The problem is not size 1 missiles, though, it's the design of the ships you're facing.
Many people, including myself, play on =<25% research rate, since that gives much more time to enjoy a single generation of ships.
"Low" tech levels can last for 80 years or more.
Even so, it shouldn't take that long to research and deploy anti-missile ECM, which you should do if you are facing a foe that overuses size 1 missiles.