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ECM isn't so important to an ATM build that you desperately need it to the point where you pick a Shadowcat over a Huntsman
It's not about ECM, it's about speed. MASC makes Shadowcat almost 1,5 times faster than Huntsman (because you mostly need this speed for short periods of time). Using ATMs on these mechs is very different. Huntsman is much more traditional, gotta-stay-with-the-deathball playstyle. With SHC you abuse the speed and try to enter the 300 m range as often as possible, flank, shoot the backs. Then you have the speed to leave the skirmishes which Huntsman would be unable to retreat from. This also means that you rely on running away more than on backup lasers against enemies who try to hug you.
Considering all this I ended up playing 3x ATM6, 1 HML, 1 Light tag. The heavy med isn't a real backup weapon here, more of a way to make your alpha a little higher in the situations when you only fire once and then return into cover. Also helps with UAVs. This build was really good for pugging, I was getting regular 700+ dmg wins with it. Then it kind of suffered from the lock-on angle nerf because you do a lot of running around mechs in 200-300m range and now lose the lock more often. But still I don't think it's worse than Huntsman these days.
Also regarding the launcher size, ATM3 and ATM6 have lower spread than ATM9 and ATM12. The gap between ATM6 and ATM9 is pretty noticeable, but I don't see the point in switching to ATM3 since the spread stays the same as in ATM6.