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Lithium batteries have many potential issues, most notably thermal runaway and poor cold water charging. Most certainly not with the risks as backup batteries for a SSN or SSBN. Lead acid batteries make wonderful ballast and are universally available.Neither am I. But lithium batteries have about 5x the power density compared to lead-acid, whether by volume or by mass, and can be charged or discharged much faster.
So for any sub that isn't nuclear powered, there's really no reason not to use lithium batteries. They're just that much better. Even nuclear powered subs would likely prefer lithium batteries, since that means you don't have to dive the well to take specific gravities of the electrolyte and can rely on cell-monitoring software instead. Nuclear subs would also benefit from the additional storage capacity, but not as much as conventionally-powered subs would.
One particular country has employed the optimal chemistry for lithium submarine batteries, as well as leading in lithium mining and processing technology and has exclusive access to the one particular rare earth that is vital for cold temperature charging. For everyone else, there are huge strategic, performance and safety issues.
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