Make nuclear submarine be able to carry nukes and act as a launch platform for these missiles. They could receive a special action, where they have to perform a "surface" move to make them more vulnerable to the one being on the wrong end of the nuke or something like that. The first time i build one of those submarines i was expecting them to be able to act as a mobile launch platform.

Yes, I'm surprised this is not a thing.

Wald

In fact, launching a nuke from a submarine should be a three step process:

Phase 1: Surface/prepare the nuke

Phase 2: Launch nuke

Phase 3: Submerge/Nuke lands

During the surface phase the sub is still invisible to units unless they stumble upon it (destroyers. Should the sub be discovered during either the first or second phase, it is attackable. If the sub is attacked during the first phase, it will cancel the nuke launch and if the sub is destroyed, the nuke is also lost. If the sub is attacked during the launch phase, the nuke will still launch to hit its intended target. Launching the nuke makes the alerts all enemy ships within a 10 hex radius. They cannot see the sub necessarily, but they will know it's exact location. In phase three the sub will submerge and be invisible as normal but only have half its movement points. Normal combat/detection rules apply.

Wald

I quite like the idea but it could probably be less complicated (halved movement points for example seems not necessary).
The three phases could be -> emerge (1 turn), shoot (1 turn), dive (no turn necessary). Emerging would be a clear sign (there's no reason to do it other that nuking). I would make the submarine more visible, at least two or three hexes away, normal for some contemporary vessels (destroyers should have no problem seeing a sub on a radar if it's surfacing). I'd take the possibility for the sub to get away after the emerge part by renouncing to shoot. However in case it shots, it should not be able to defend itself. No more than x nukes on a submarine and range smaller than an intercontinental missile. A cooldown between launches would be good too (as terrean silos get them).