They did say in the first Matrix that the energy from the humans, combined with a form of fusion gave them all the energy they needed. Since it's a few centuries in the future, it's conceivable that technological advancements that we can't imagine now are possible then which would make it more efficient to use humans like batteries in this way.
In these kind of movies portraying future tech, there will never be a step by step detailed explanation of some unthought of technology that actually works in the real world or we would get on creating it asap. It will generally just be at best a interesting idea that may inspire some research or inventions in the future,
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