Lithium batteries do get ever so slightly heavier when charged, but it's basically undetectable.
The mass associated with those chemical bonds is miniscule compared to the protons, electrons, and neutrons, but it is not zero.
Ah, but it is. E=mc^2 is always true in the reference frame where the object is stationary. (We assume that we are co-moving with the windup car.) A spring under torsion is heavier than an unwound spring.
Does it have more (invariant) mass?
100% of the mass difference is converted into energy.
I agree, if you're deploying 1 kg of fissile material, only 0.1% of that will be converted to energy. We should talk about energy per mass of fissile material, not energy per mass of "mass difference".
Nuclear batteries are extremely reliable though, as they are fully solid state. A Pu-238 battery can emit useful amounts of power for upwards of a century, and there is virtually nothing to break.