In my current game I'm not allowing myself to use missiles, so I haven't experimented much with them, but I'm coming to appreciate the utility of ECM and ECCM. I'm considering using a more balanced doctrine in my next game, when 2.0 comes out, so I'm starting to think about how ECM/ECCM works for missiles. So far pretty much all I know for sure is that when you put an ECM or ECCM module on a missile, it takes up 0.25 missile size points (total of 0.5 if you put both).
I assume when you put ECM on a missile, the missile becomes harder to hit, improving its survivability vs the target fleet's AMMs and PD turrets. This generally seems like a good idea as long as .25 size points is worth more of a reduction in intercept (based on your relative ECM level to the enemy's ECCM level) vs the improvement you could get with an extra .25 size points of engine or agility. However, if you know the enemy has equal or better ECCM, you may as well leave your ECM off and use the extra space on the missile for better speed/fuel/warhead/whatever.
Concerning putting ECCM on a missile... does that neutralize the target ship's ECM, meaning your missile does better than it otherwise would against targets with ECM? Can you achieve the same effect by assigning an ECCM to your launching ship's Missile Fire Controller for the missile's launcher, and if so, wouldn't you always prefer to save the size points/resources on the missile by putting the ECCM on the ship? Or does missile-based ECCM only apply if you also have an active sensor on the missile and it detects the target?