I only ever use chaff, because they are good to lose missiles, and also effect gimbals and turrets, so 3 in 1 tool, why waste any more slots than you have to. Use spare slots for shield boosters if you have the power.
whats strange, is that missiles are supposed to be heat seakers, aka chaff should not having any impact. At the same time, ECM then makes no sense either.
i only fit point-defense when going into a conflict zone, because the cobras there drop mines here and there.
you can manually shoot down missiles too. so if you have a "turret" mounted, you can select any missile with the "highest threat" lock and let the turret take care of it.
so, for countermeasures:
ECM only works against seaker missile and torpedos, but is cumbersome to use
PD works against seaker, dumbfire, torpedo and mines
Manually shooting works against all of them, but is tricky
heat-sink / stealth works against any target lock
chaff - cannot confirm that it does anything