Submarines need oxygen. If you are using your oxygen for both burning fuel and the crew, you run low on oxygen, you need to resurface before you run out, and both your engine and crew die.
Submarines need to stay undetected, so if you use a fuel that doesn’t need oxygen (nuclear), you extend the amount of time you can stay under significantly.
Aircraft carriers are big and use a lot of power, so they can effectively make use of a nuclear reactor.
Smaller ships don’t have the niche need for a Submarine sized nuclear reactor and aren’t big enough to need an aircraft carrier nuclear reactor, so fossil fuels are sufficient to meet their needs.
It’s basically just a matter of “why use a sledgehammer when a hammer works just fine” except you don’t have the risk of a nuclear disaster at sea
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