Marines are used as reaction forces for small flare ups on carriers, usually acting as guards for weapon storage and visiting vips (both to make sure they are not getting lost (lost or spying) and to protect them incase somehow a hostile force gets onboard), or so I have been told by some marine friends. Submarines do not carry a complement of marines and the only time that I saw them onboard was when they were doing a walk thru for familiarization incase the ship got taken and they had to retake the ship. They were on the pier and the hills surrounding the explosive handling warf when ever we were onloading or offloading our slbms, from the chief: dont go up there unless you have a good reason and if they yell at you to stop, stop, get on the ground if they need you to do so and just do what they say, I dont need my guys full of holes b/c your being stupid." :ar15 :splat :flame
Don't think any amphibs are nuke powered and they retired all the nuke crusiers, DD, and FF.