Had a quick look in the designer and as far as I can see;

A: your 1m Mantlet's for the main guns are mounted horizontally, and your guns are on a turret, so horizontally mounted mantlets don't give you anything your turret isn't already.
B: You have your main guns setup as Railguns, with no "Rail Draw" set for the gun to propel the projectile, so essentially your shells are just dropping out of the end of the barrels.
C: to make that issue worse, even if you add Rail Draw to your firing pieces, there is no space in your turrets to add enough "Rail Chargers"
D: Your Main guns also don't have enough recoil compensation, there is "some" but when you look at the stats of the gun, it usually has an amount per second listed, if you don't match that the gun will get more and more inaccurate as it fires, becomes akin to a shotgun the longer it fires for.

This could be somewhat "fixed" by reverting the guns to none Rail types and swapping out the Mantlets for larger ones, maybe the 3m Vertical. Also by adding back the Gunpowder Casings for the projectile.

The reason your guns just twitch and either miss horribly or don't fire at all is that the AI is trying to elevate the gun to allow the very slow projectile to hit it's target, but it cannot so it never gets to a position it can fire to hit the target, so it doesn't fire at all. This also happens if you take manual control of the turret, it just can't elevate to where it needs to.

With how low in the water your ship sits, I think most of your detection equipment might be too low for it to see the target well enough, I usually add some detection to each turret as well and even mount a suite of detection equipment on it's own turret with no guns, if you then AI control that "turret" it will point all your radar and camera's at whatever target it picks first.

I realise by this point you have either figured all this out yourself or just stopped playing From the Depths entirely, but I'm a sucker for forum threads asking a question with no replies ^^. I am also no expert in most of the systems in FtD but I'm slowly learning :)

Cheers.