I am guessing at one point missles and fighters were MUCH more difficult to destroy, and had sharper teeth, but at this point in the game they are very weak. A primary issue is that medium weapon mounts can actually hit them (defending fleet turtles, rides out the 2 or 3 waves, mops up). Perhaps only point defense systems should be able to destroy missles/fighters? (point defense including interceptors, and anti missle systems).
If I am understanding right, Heavy weapons mounts are spinal mounts (no equal on current ships), Medium mounts are the equal of current heavy anti ship turrets (think IRL battleship turrets), and point defense are the smaller guns that have more mobility and can hit anything but at a shorter range. I would be very interested to test a build like this, assuming it wasn't a nightmare to make.