I don't think weight is a huge issue for submarines (unlike say airplanes), so taking a few batteries along should be fine.

(I don't know anything about subs) you could even store a few batteries in the ballast.

Between "waste some power on a magnet" and "we're permanently stuck on the bottom of the ocean about to run out of air", I know which one I'd pick.

There's a difference between a "waste of energy" and a failsafe emergency system that happens to use a lot of energy.

It's nothing compared to amount of power to the engines, you don't need kilowatts to "just" hold a ballast

Clear tradeoff for safety.