Proximity charges work best when not fired at any missile in particular, but rather thrown at the enemies en masse to create an unpenetrable wall of PD that also deals damage. For that end, targeting ships works better than targeting fighters or missiles.
Except in non-frontal facing missile setups, such as the Apogee, or the Conquest since it broadsides. This results in the missiles coming in at an angle that prevents the PCLs from destroying them.
Likewise, once the PCLs are out of range of the enemy ship, they stop firing, which means enemy missiles are uncontested.
I know having PCLs target missiles works and works well because I made a mod for myself, back before Alex fixed them. The mod fixed the EECM issue, and set launch speed to travel speed and lowered both. They were the Odyssey's only reliable answer to both the Conquest and Onslaught. With the exception of double Tachyon lance, squalls, and A.I. engagement range manipulation.
@Brainwright
There was a bug with EECM last version that reduced PCL range and speed, technically it increased acceleration which, due to PCLs launching faster than their max speed, increased deacceleration.
PCLs on any ship that lacked EECM last version were, for the most part, fine.