Why do two 6 volt batteries in series usually have more amphours then a single 12 volt battery?
I can't say as I've noticed this myself, but it seems likely that the probable answer--assuming your premise is correct--is that the total capacity of the two 6-V batteries is greater than that of the 12-V one.
All else being equal (total battery mass, not counting packaging, of two 6V batteries being the same as the one 12V, same battery technology, same manufacturing design of cells, etc.) there is no reason the storage capacity would be different. There might be some subtle practical reasons that make them slightly different, like heat dissipation being a little better with two smaller batteries than one big battery, but it wouldn't be a notable difference. If you have an example of a notable difference, then I would strongly suspect its a different technology, notably different design parameters, etc..
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