I've been on a bit of a swarm LRM trip lately, haven't I? Though in my defense, they really are one of the more "complicated" ammo types, raising questions that those that only care about one target at a time generally just don't.
Anyway: the last bullet point on page 371 states that anti-missile systems function "normally" against Swarm and Swarm-I LRMs. Okay, so that first of all means they can engage them and inflict their cluster penalty...
...what does that say about any followup secondary attacks, though? Fluff-wise, the cluster penalty presumably reflects the AMS shooting down some incoming missiles, meaning that they really shouldn't be available for purposes of going after nearby targets of opportunity anymore either. But the stock AMS rules don't really make that sort of fine distinction on a mechanical level, they just turn more "hits" on the cluster table into "misses", which are then in turn exactly what Swarm/Swarm-I LRMs base their secondary attack volley sizes on...
So: what's considered "normal" here? If, for example, an LRM 15 launches a Swarm salvo at a target and an active AMS on the latter's side duly reduces the cluster roll from an 10 (twelve hits) to a 6 (only nine) -- how many missiles does that leave to make a secondary attack with? Fluff would seem to suggest three (the original ones that never found the target in the first place) while mechanics would indicate six (because after applying the penalty only nine did hit and 15 - 9 = 6, dangit, even if that means that the three notionally just shot down have to spontaneously reassemble themselves in mid-air)...