Sounds like I've missed discussion on a lot of fun changes!
If this sounds like a huge boost for missiles, it is. However, I also plan on adding some form of ship-deployed decoy to distract missiles, which will be much larger and more costly, but will affect all missiles heading for the parent ship. I may also add a form of fragmentation warhead to missiles, that would be ineffective against ships but able to eliminate decoys and small missiles.
It took me some time to fully wrap my head around this change, since I mentally wanted to handle it like the old ECM vs ECCM system, where having ECCM 3 countered ECM 3. But it's worded as a reduction if the ship has an ECCM advantage, which means equal levels do *not* counter each other out. What's more, even if the ship does have an ECCM advantage reducing the number of decoys by 1 does not necessarily negate *all* decoys. So yeah, that seems like a pretty powerful change. I think we might be approaching the era of big honking anti-ship missiles with tricked out subsystems (I'm not opposed to this).
I know you mention decoys for ships (it would be interesting to me if the size of ship decoys was proportional to the ship size, cloaking device style, which might give a little more role for anti-missile escort ships), and after thinking about it that's probably important to provide a ship-side version of the new EW mechanics. But I was also thinking if testing shows this change favors missiles too much, the recent addition of partial warhead damage means you could also do something similar for dedicated ship based point defense weapons - a 6 cm anti-missile laser doing .5 damage and such.