That's an issue with missile specials being kind of terrible ATM, in my strong opinion (see as well Alpha Strike making Artemis 'Mechs immune to ECM and AMS).
How exactly are Artemis-equipped 'Mechs immune to AMS? AMS makes you subtract 1 point of damage (minimum damage of 1) from any unit that has the IF#, SRM#, or LRM# special abilities, & not just when using those special abilities but for regular attacks as well (AS:CE, p. 76). Note that the errata for Point-Defense (AS:CE, p. 88) modifies the last paragraph to have 1 point of PD be treated against IF#/SRM#/LRM#-equipped units as if AMS was used. And granted, ECM doesn't have it listed, but the same rule could easily be added, since ECM blocks the extra +1 damage that Narc/iNarc pods provide. Remember, the effect of a Narc/iNarc pod for a non-Artemis launcher in CBT is identical to the effect of Artemis on a launcher (+2 on the Cluster Hits table), so the effect on ECM in AS on Artemis should be the same as on Narc/iNarc attacks.
Now...if you mean that it's because Artemis-equipped units aren't
identified in Alpha Strike, then the solution is simple: add an ART special ability for all units that have Artemis-equipped LRM/SRM/MML/ATM launchers.
What I find more strange, actually, is that despite ATMs having three different types of ammo (& therefore different damage profiles like an MML), they don't have some sort of different damage profile for a "special" attack. Essentially, they could have something similar to "SRM#/#" and "LRM#/#/#" values, representing the use of HE or ER ammo...but they don't.
