The way I see it is that it's not that missiles are too strong or too weak, it's that they're too binary. It's very easy to get in a situation where you launch a huge salvo of missiles and every single one gets shot down. It's also very easy for a player to come up with tactics that help bypass the PD, like box launchers and massive salvos, in which case missiles can be absolutely devastating.
I have a few thoughts on things that might help with this.
A) Point defense could be less all or nothing. Basically, instead of point defense that can shoot down 60 missiles moving at 30,000km/s, I think it would be interesting if that same point defense setup could instead shoot down 60% of the first 100 missiles moving at 30,000km/s. Basically, find a way to make it "leaky", in that at least a few missiles often get through. Mathmatically, this probably means something like making it so each missile only gets shot at once/twice/etc no matter how many guns you have, or at least the game goes "there are 20 missiles and 30 point defense guns, so 10 missiles get shot at twice and 10 missiles get shot at once. Now making chance to hit rolls" instead of assuming exactly enough guns fire to hit each missile and then move on to the next.
B) I'd like to see laser warheads come back, by which I mean missiles that do less damage but bypass the final defensive fire phase of point defense.
C) It would be best if the AI used at least a few tricks to better penetrate PD, like box launchers/reduced fire rate launchers or (if B is implemented) having some salvos consist of laser warheads.