I've played this game for a while now and had a lot of time and experience testing different classes, with different loadouts and modules, and here are a few notes I have about Missile/Torpedo modules (on both Destroyers and Dreadnoughts) and about Dreadnought modules in general (mostly relevant to the T4-5 range when all modules are unlocked). Also I don't know how to tab paragraphs in this thing or bold or anything like that so sorry for the monotony.
There are a lot of options out there for missiles and torpedoes between Destroyers and Dreadnoughts, but some are far more useful than others, and here are my reasons for thinking so.
Storm Missiles- First thing's first, these things are ridiculous. Almost 30k damage from 3000 meters at T4 on a 50 second cooldown, plus they travel quickly and all fire at the same instant. Even with shields up, these monsters usually kill anything but a T4 Dreadnought without question, much more so when you throw a Drain Torpedo first. I'd either reduce the range, increase the cooldown, or reduce the damage. As is they're just too reliable and overshadow all other primary missile/torpedo modules at T4 besides the Goliath. Compare them to Flashpoint Torpedo Salvo, which does a max of 20k damage at 1200 meters, with a 40 second cooldown, plus they can be dodged much more reliably.
Tempest/Vulture Missiles- I find the balance on these ones to be alright in terms of damage, range, and cooldown. However, their tracking is so bad that nine times out of ten they fail to hit anything that isn't a stationary Jutland. A slight wiggle from most ships is all it take for them to miss completely, and if you just scoot back and forth, up and down, you can easily make them circle around you until they blow up on their own. Or you can just outrun them because they're so damned slow. I'd up their flight characteristics just a scooch to make them relevant, but it's not really a big issue.
(I'll cover Dreadnought secondary missiles/torpedoes in the Dreadnought Module section)
Primaries- The only issues I find here are Scattergun Broadsides; they're pretty much useless. I tried them with several builds and wanted so much to make them work, but they just don't. They take too long to fire, offsetting most of the difference in cooldown between them and Ballistic Broadsides, plus their insanely limited range means they almost never have a chance to be fired at all. Additionally, they're far less potent against Corvettes than Plasma Broadsides. I'd up the range to 1200 meters and make them fire faster, to make them the real close range DPS option.
Secondaries- Light Missiles. They're pretty much the only relevant secondary for Dreadnoughts, and I've tried them all (except Triad Pods but 315 DPS on a destroyable pod? Please.). Their balance between range, speed, damage, and cooldown makes all other options irrelevant, as each other option has some glaring issue. Vultures never hit anything because they're so slow, the torpedoes take so long to launch and track so poorly that they, too, never hit anything, and Flechettes take 10 seconds to fire off for some reason, which is absurdly long for a missile system intended for close range and rapid flight time. Light missiles fire fairly quickly, deal good damage, track very well, and have a low cooldown. I would make Dreadnought torpedoes deploy a bit faster and track a bit better, Flechettes should take at most 6 seconds to fire all missiles, and Vultures I've already talked about. I tried to make the other options work on my Lorica but Light Missiles seem to be the only one that gets consistent results.
Perimeter- I have no issues here- each option is useful to the right build(s).
Internal- One, Assault Thrusters. I like them and they're useful but the second your ship nicks anything they turn off, plus you almost completely lose the ability to turn when using them and are stuck flying forward (you actually can't stop without disabling the boost first). Warp Jump is almost always better for getting place to place, especially at T4 when you can jump straight to any target within 5km, regardless of where your ship is facing.
Two, Endurance mode. I don't honestly know why it exists. If, when you activated it, you remained at the same percentage health as you already were at, then I'd be on board, but as is it's pretty useless given the nature of DPS battles. If you're being healed faster than you're taking damage, you don't need the extra max health, and if you're taking damage faster than you're being healed, you'll never get to use that max health anyway. It's pretty much just wasted space when you consider how useful the other internals are.
Finally, and most importantly, Armour Amplifier. This is my favourite Dreadnought module in the game, but for some reason it gets considerably worse as you upgrade it. I still use the T3 version on my Lorica, and if I could use the T2, I would. The cut in duration as you rank up is WAY to significant, especially when you consider that the cooldown only drops by 10 seconds from rank 2 to 5. In a prolonged battle, assuming consistent damage over time and you have it up as frequently as possible, here's the math:
Rank 2: 80% reduction for 15 seconds on a 35 second cooldown. Net reduction of 24%. (As an added bonus, you are able to recharge most of your energy while the module is active such that you can shield when it goes down, thereby further increasing your damage absorption.)
Rank 3: 85% reduction for 12.5 seconds on a 33 second cooldown. Net reduction of 23.3%.
Rank 4: 90% reduction for 10 seconds on a 30 second cooldown. Net reduction of 22.5% (At this point you don't have time to charge you shields much over the duration of the module, meaning you will take much more damage after it wears off if you didn't already have energy banked.)
Rank 5: 99% reduction for 5 seconds on a 25 second cooldown. Net reduction of 16.5%. (Over 5 seconds you can barely charge any energy, so the rank 5 armour amp offers no time to regain shields.)
(This is my math btw I just put it in this box to make it stand out)
So basically, not only does the net absorption drop, especially at rank 5, but you also have no time to regen energy. The way I use Armour Amplifier is this: I use shields until I'm just about out of energy, then activate the module and drop shields. Over the duration (at rank 3 on the Lorica), I regain most of my energy over the 12.5 second duration. Once that wears off, I reactivate my shields. If I upgrade to rank 4, my ability to regen energy is cut a bit (down 2.5 seconds), so I'll take more damage than I would if I stuck with rank 3. At rank 5, I can't really regen anything so if I'm not out of trouble by the time the module wears off, I'm boned.
My main point is this: Dreadnoughts are usually employed to tank damage for the team over as long a time as they possibly can. This means that 15 seconds of 80% reduction is far more useful than 5 seconds of 99% reduction, both for yourself and the team, as it allows you to soak up damage for a longer time and keep enemy fire focused on you. With 99% reduction, a smart enemy will just retarget to someone else because they're doing nothing shooting at you, putting your teammates in more danger. Plus the duration is so low that you'll likely have to duck for cover when it wears off as you won't have shields, further reducing your tanking effectiveness.
I would keep the duration across all levels locked in at somewhere from 10 to 12.5 seconds, and scale absorption from 75-80% at rank 2 to 85-90% at rank 5, while maintaining the current cooldown scaling. I think this is a good way to give the rank 2 module the slight nerf I think it could use, and to make the rank 5 version actually superior.
Anyway, those are all of my balancing notes on those issues. Thanks for reading and let me know if you agree.