If you're going to start introducing CNT-based armor, then likely.
Assuming we are talking about a battleship or cruiser armed with a heavy gun-based artillery battery.
In those cases, the turret roofs are the easiest vulnerability to hit for precision missiles.
Of course, directly answering your question, ALL incoming munitions are better dealt with by hard-killing the munition/source or evading it, it doesn't matter if it's an ASBM, and AShM, or a 7.62mm someone is standing on a boat shooting at you with.
This is where the old 'Threat Onion' comes into play.
For a Warship in the missile age, it is:
Don't be Seen (Evade the Threat), Don't be Targeted (Spoof the Threat), Don't be Hit (Kill the Threat), Don't be Penetrated (Block the Threat), Don't be Killed (Survive the Threat).
Armor is in the 4th Layer, which is basically the last layer if you're trying to prevent serious damage.
Ideally, you defeat the threat on a layer further out on the onion.
Of course, something will
get through, even if it's just fragmentation. Armor is to protect against that inevitability being the fatal blow.
You're right, that's a topic that would require entire libraries to actually convey with 100% accuracy; libraries full of books I am not qualified to write.
However, in the most general of terms...
If you're talking a ship utilizing supermaterials such as CNT nanoplates, it depends on how much you intend to armor and what you are trying to do with that armor.
If you're just trying to protect the vitals of the ship in order to prevent a complete loss, then the armor would be boxes around the vitals - much like the all-or-nothing scheme of yesteryear.
If your point is to prevent as much crew death as possible, then the armor would essentially be built into the hull and superstructure of the ship - it would look like what the exterior of the ship looks like, just set in a little with internal boxes around the components that must be exposed to the outside (such as radar). This would also prevent a complete loss of the ship, but the ship could be rendered blind, deaf, and dumb by critical hits on the exposed electronics. Strategic weapon systems and heavy gun-based artillery likely would still work however, so if your ship's purpose is throwing strategic munitions at fixed targets, this would likely prevent a mission kill.
If you are trying to prevent mission kills for tactical systems (the goal of the armor in yesteryear), you encounter the reason why Modern Navies gave up on armor (aside from the weight).
Modern Navies don't see the point in armor because the difficulty in armoring the abundance of externally mounted sensitive electronics such as the massive radar panels that have become bog standard anymore, most of which could easily be destroyed with as little as a hand grenade or the smallest shard of fragmentation.
Armoring the Radar is
actually possible as well, but armored electronics have to either be 'peek-a-boo' style or mammothian. In either case, their effective power per unit of volume is going to be drastically lower than the exposed type, making the resulting ship a veritable leviathan if you intend for it to have comparable signals/ECM power to the more vulnerable ships.
It's entirely possible, though; especially if you're willing to accept more limited sensors on the ship, it would just be extremely expensive and time consuming to build and operate.