the problem with missiles is they have extremely low alpha damage(in that the time between firing and damage caused is so long their DPS suffers greatly). their damage is effectively delayed and damage that was in queue to kill a ship that get's destroyed vanishes. This overall makes missiles just a problem from any angle you attack them from unless you change how missiles physically behave in-game.
Missiles effectively turn into this kinda DoT with a delay on them. Honestly if they just increased their speed significantly they'd probably be reasonably fine. their niche is they rarely miss, which would stay if they just increased missile speed. This woudl also give PD less chance to shoot them down.