As far as I can see, missiles have three major things blocking them from receiving any potential buffs.
Firstly, they suffer a bit from overpowered secondary effects. Not to the same degree as railguns and definitely not as much as torpedoes, but they definitely have some of the stronger ones. Some of the stronger secondaries might need a bit of downward tweaking (whether reducing their benefits or upping their drawbacks) to give additional headroom for other buffs to become possible as having a weapon with both powerful utility and high damage potential is quite a dangerous thing.
Secondly, Packhounds are a problem in terms of balancing missiles. They are so much more powerful and more effective than regular missiles in having more than 3 times the DPS as well as being much more reliable at hitting fast moving targets or applying secondary effects repeatedly. Compared to the sidegrades that are the rest of the powerplay modules, they are a definite outlier on the power spectrum as they are almost strict upgrade. This power level means that sweeping buffs to missiles in general can't really be done, although some buffs to bring regular missiles up to Packhound level might be an option.
Thirdly, synthesis is a problem for any weapon that is meant to be limited by ammunition. Because synthesis is so easy and convenient, it practically renders ammunition irrelevant from a balancing perspective as any weapon with synthesis has practically infinite ammunition. This obviously causes problems for regular kinetic weapons, but for a weapon like a missile rack that is meant to be primarily ammunition limited it requires them to be barely more powerful than regular weapons. As the age old balancing mantra goes: "a drawback that can be trivially mitigated is not a drawback at all". To be honest, I feel that synthesis needs a full rework in order to be a useful and balanced mechanic, rather than the current implementation of "material-fuelled cheatcodes".
I don't think a massive sweeping change like giving missiles their own hardpoints is the solution, there's definitely design space for players to choose between high alpha strike potential (explosives), high combat endurance (lasers) and somewhere in the middle (kinetics). Separating out the weapon slots between ordnance and regular weapons would effectively remove combat endurance on weapons as a variable, as all ships could effectively max out on both sustained damage and burst damage as they would rely on different slots. It's the same reason why I argue against putting HRPs into sub-slots in the bulkheads or restricting them to military slots, as it would remove all choice between HRPs vs utility vs shield reinforcement vs SCBs as then every player would have both max HRP and max "other".
So my suggestions for missiles would be simple: Remove the ability to synthesise ammunition for them, buff regular seekers up to packhound levels in terms of DPS, pending beta testing potentially buff damage on missiles further, check to make sure secondaries are not being too overbearing and buff up damage numbers on dumbfire missiles to keep them hurting more than seekers.