I have long said that there should be a check of the (CM_speed+inbound_speed)*5s and if the range is less than that between them just check for the interception as the two missiles are on converging courses it is not like it matters which one is faster.
This would require a complete change of game mechanics. Or at least a significant rewrite because of how Steve originally wrote the game to work. Every mobile object moves from point A to B, and only after that are others things checked. Inserting a minimum distance for AMMs is probably easier and faster.
Also so far as I can see the technology that increases your tracking speed the longer you track a missile doesn't work.
Correct, it's broken in 7.1 but fixed for C#. This is one reason why tracking speed issues exist. But even with tracking speed issues, it isn't impossible to create impossible to penetrate PD screens by stacking cheap railguns.
More annoying is that the magic missiles are counter missiles themselves.
Yes, intercepting AMMs is probably THE most annoying thing in Aurora combat currently. And even if they do cause only 1 point of damage per missile, NPRs/spoilers often fire thousands of them at you meaning that sandblasting eventually gets through any and every player ship. And Steve can't just have the AI not use size 1 missiles offensively, because what if they are the only weapon available to the AI in certain situations? There are solutions to counter it, especially from orbital bases, where you soak the damage by sending in cheap commercial ships that are nothing but massive engines and cargo holds - or any other high HTK cheap BP components. Remember that large engines can survive, due to how HTK and damage are calculated, extraordinary amount of punishment.