there is the Watchdog which is the ECM/AP but not C3 equipped version of the Nova gear.
Not
quite, since Nova still overpowers basically anything. I'd imagine they'd develop ECM/AP suite(s) that are at least up to par with that, if only just in case someone decides to start using Nova again. It would also give them, at least for a time, an uncontested edge in shutting down C3, enemy ECM lances, stealth armor ambushes, and other well-known IS dezgra tactics.
I don't see ER Pulses catching on however
Yeah, me neither, but I figure if anyone might have a few left over it might be the Lions. I'd more expect them to give iHLs a whirl.
and imagine the iATMs were kept pretty close to the chest (and unfun in the tabletop game)
If memory serves, iATMs were one of the pieces of Society tech that the Lions were allowed to dissect (if memory serves under the agreement that they would share their results with the High Council and, by extension, the rest of the Clans). As for the balance, yeah, they were really rough against the Clans, but there's two factors that I think would temper them in the event of a Clan Invasion 2. First, IMP and IIW almost certainly wouldn't make a comeback; granted, they're not the reason everyone fears iATMs, but they still offer quite a lot in their ability to debilitate opponents. Second, and perhaps more importantly, is the relative prevalence of Angel ECM in the Inner Sphere by now—said ECM being able to turn Streak missiles into standard Cluster Hits-rolling plebs, without even the Artemis bonus of standard ATMs. Assuming the ECCM from the aforementioned hypothetical ECM suite doesn't cover the whole dadgum map, there is at least one huge counter to iATMs that can be reasonably reliably obtained by any IS faction. Throw in an AMS for good measure, and even HE iATMs can be dealt with fairly reasonably.
EDIT: Oh, and apparently RISC Viral Jammers, for as uncommon as they are, counter Nova, by the way.