Long post in which I discuss what I think a balance problem is with missiles, as well as a possible solution. If you're interested, please read the whole thing and don't take a quote out of context!
To start, let me say that I believe that missiles are an incredibly overpowered weapon. The missile launcher has the best burst damage in the game, the best splash in the game, the best range in the game, is the only indirect fire weapon, is the only guided weapon, and still has moderate continuous-fire dps. Compared to any other weapon, the missile launcher is clearly stronger. However, point defense is incredibly overpowered too. 10 point defenses (+power, crew) costs around $40k. 10 missile launchers (+power, crew, factories) costs around $400k. Yet, 10 point defense can reliably shoot down 10 missile launchers, whether they volley or continuous fire (which I just tested). That gives PD 10 to 1 cost efficiency. Contrast that to shields, which have roughly 1-1 or 2-1 cost efficiency.
The result of OP missiles and OP anti-missiles is an extremely binary weapon. If your missiles can overwhelm my PD (which, don't forget, takes more than 10X the cost), you almost always win because no other defense stands a chance vs missiles. If I have enough pd to shoot down your missiles, you almost always lose because your weapon cost 10 times what I spent to stop it.
This boom or bust behavior of missiles means that you need plenty of PD in case the enemy has missiles, but the enemy never brings missiles because they know you'll have PD. This also leads to games that are won or lost on the ship select screen.
So, why not reduce the power of missiles while also reducing their vulnerability to PD? By splitting the missile launcher into 2 separate weapons, each one can inherit some of the old launcher's strengths without being too strong individually. I suggest breaking the missile launcher into 1) the cruise missile and 2) the torpedo.
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Cruise Missiles
The cruise missile would inherit the long range, precision guidance, and indirect fire nature of the current missile. Cruise missiles would have greatly reduced shield damage (e.g. 4800->2000), would only store 1 missile per launcher, would have a larger hitbox than existing missiles, and would cost slightly more missile parts (e.g. 4->5). Cruise missiles would also fly faster, turn quicker, have improved guidance (when Walt get around to adding it), take multiple PD shots to destroy, and could possibly be retargetable while in-flight or have other fancy control options.
These missiles would be great for picking off pesky swarmers or for wrapping around an enemy to get at the exposed engines behind. However, they would have a low fire rate, would be unable to burst-fire, and would no longer cut through shields like a hot knife through butter (though splash through shields would be unchanged). Speed and durability makes them less vulnerable to PD, but increased missile part cost and reduced shield damage makes them less deadly against regular defenses.
Cruise missiles could replace existing missile launchers so that nobody's ship designs break, since they are more similar to the current missile launcher.
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Torpedos
Torpedoes would inherit the burst fire and terrible, terrible damage of the current missile. Torpedoes would have medium/short range (e.g. 250->175), minimal guidance, reduced splash damage, slightly reduced shield damage, and slow projectiles (possibly with deceleration over time). Torpedoes would also store many more missiles per launcher (e.g. 3->6), would take slightly fewer missile parts (e.g. 4->3), and would have a cheaper launcher (e.g. $12000->$8000).
These would be great against large, slow capital ships, and would be strongest when carried on nimble fighters that can dart in close, unleash a torpedo barrage, then back out to reload. However, they would only have moderate continuous-fire dps, and would be hampered by their short range, lack of guidance, and slow projectile speed. This makes them difficult to aim at an enemy and easy for PD to shoot down, but the size of a barrage as well as the close range would help make up for that vulnerability. The more PD or more engines an enemy has, the closer to their guns you'd need to get for an effective torpedo barrage - but you're not straight-up SOL just because they have some PD.
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Also, I realize that there are more missile types planned on the roadmap, but IMO they would not impact the way current missile launchers are used (except possibly to make ships have even more PD).
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TLDR: I think both missiles and PD are too strong right now, leading to very boom-or-bust ship designs. Straight-up nerfing both missiles and PD would remove some fun elements from the game (deadly volleys, effective indirect fire, etc.), so I suggest splitting missiles into 2 weapons, each with its own strengths and weaknesses, and both of which would be less vulnerable to PD but less deadly against ordinary defenses.