At the moment with FS2 Open, point defense weapons seem to indiscriminately target fighters and bombs. The idea behind this suggesting is allowing for modders to have some more control over this behavior than the current setup, so that layered defenses could be done.
It breaks down to two new weapons flags, which could build upon the $huge turret weapons ignore bombs: ai_profile code.
When a weapon has the bombs only flag, it is dedicated to only attacking bombs and will not fire at any other target.
Ignore bombs is the opposite, under no circumstances will this weapon ever fire at a bomb.
This would allow for instance a ship with two layers of point defense:
Point defense lasers (beam weapons with "bombs only")
Pulse anti-fighter defense ("small only" "ignore bombs")
Attaching these flags to say secondary weapons could allow for the 'interceptors' from Babylon 5 which only target projectiles aimed at EA ships.