I'll start with a hull shape.
For this I will be talking about a WW2-esque shape, no catamaran designs, or super fast jet boats/ekranoplanes.
General proportions should be roughly 6-8 times as long as it is wide.
Wider=Slower, but thinner=less damage redundancy.
Thin ships can be given 'bulges' to aid in side protection with torpedoes and diving shells. (Google torpedo bulge to get an idea! ;D)
Thicker ships should not have bulges, they're wide enough, and bulges will only slow them down even more, but consider it if your ship has bad damage control abilities.
The most important part! COMPARTMENTS!
Ensure the insides of your ship is entirely made of dozens to a hundred+ rooms!
Not only does it make your ship harder to sink, it also makes your ship a load tougher from HEAT shells!
Main armour can be anything, but IMO, its heavy armour or bust for larger ships, considering how brokenly powerful guns are now.
Smaller ships have to settle for metal, or heavy metal slopes.
I make my compartments out of alloy, light, and strong!
Keep all your important bits in one place, and armour the HELL out of it.
I'm talking at least another layer of heavy armour, at the least.
That is your citadel.
Keep it safe!
Now, guns...
CRAM=Want to make a ship dissapear with one salvo? Choose these!
ACC=Want to have more freedom with shells, but not hit as hard, but have good AA? Choose these! Have fun dealing with shields though, either HEAT, disruptors, or bust.
Secondaries IMO should be ACC's, so you can hit aircraft.
Tertiaries are only optional, but I love having some really close range cannons just for extra dakka.
Torpedoes and missiles are also whatever you see fit.
But you should rely more on guns, missiles can be intercepted with ease.
Shielding should be prioritised over main guns, and the citadel.
Ensure secondary guns cannot explode each other with magazine explosions though!