Most batteries can survive an EMP of any magnitude without being damaged, their lack of sensitive chips or antennas prevents them from picking up the Electromagnetic Pulse so they would not be affected. We know what an Electromagnetic Pulse does and what would be affected by an EMP attack thanks to an experiment the United States conducted in 1962.
In 1962 the United States detonated a bomb high above the Pacific Ocean. The experiment was called "Starfish Prime". They were testing what would be the effects of a nuclear explosion on the far continent.
Discover magazine described the results in its article on the 50th anniversary experiments. They included:
Presence of a bright aurora in the sky
Street lights burned out in Hawaii
Radio system failures
Strange electrical surges on airplanes
Damaged electronic devices
An Artificial Radiation Belt was generated
The test showed no evidence that the EMP pulse affected the batteries. Instead, they found that it fries sensitive electrical components.
This is true for all common types of batteries, including lead-acid, lithium-ion, alkaline, and nickel-metal hydride. Only complex battery modules with integrated charge controllers are likely to be affected.
The EMP sends a surge of electromagnetic energy throughout the electrical grid. Electrical components absorb that energy through antennas or wiring. The result is massive energy overload damage.
The EMP can even damage components when they are not connected to the network at all.
Instead of draining batteries, the EMP fries sensitive components in electrical devices...unless that device is shielded from its electromagnetic field (EMF).
Will an EMP Destroy Batteries?
No. Your batteries will survive. Their lack of sensitive chips or antennas prevents them from picking up the EMF.
However, nobody does high-altitude detonation experiments anymore. The last test was in 1962. More than 50 years ago. Since then, we have all kinds of new batteries available, including lithium and rechargeable batteries.
Car batteries should work, but because the EMP fries the sensitive electronics inside the car, it won't work anymore.
Not all cars will fail. Some older cars encase their electronic component in steel. The steel absorbs the EMF pulse, protecting your electronic components. This steel enclosure is a "Faraday cage".
So yes, your batteries should be fine if you hit an EMP.
Still Not Sure Your Batteries Will Survive?
To protect your batteries and other sensitive electronics, place them in a Faraday cage. A Faraday cage can be any container made of conductive material. The cage absorbs the surge of energy from the EMP. This prevents the pulse from reaching the sensitive electronics inside.
In a pinch, use your unplugged microwave as a makeshift Faraday cage. Just be sure to cover the door with the viewing screen with aluminum foil.