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At the risk of speaking for the parent, I believe their point was that the only fusion "reactors" on a nuclear submarine are the warheads it carries.

Maybe you're just less bothered than I about the writer conflating fission and fusion when the difference between them makes for a good deal of the newsworthiness of the article.

I'm well aware of the fission reactors in large military ships, but if there is any application of nuclear fusion on them then pretty much the only option today is thermonuclear warheads. It would be really nice if that's about to change.

Most warheads have hollow plutonium pits that are filled with tritium (right before implosion) triggering a fusion reaction from the high heat of the plutonium fission reaction. So no, it's not only the H-Bombs, though those are primarily fusion while tritium is only used to "boost" classic implosion fission warheads.

He's making a joke about how fusion has been used successfully for decades, but only for bombs. Thus, aircraft carriers and submarines do have fusion devices on board, but they're only used for destructive purposes.