Your question doesn't make sense (no offense). How come she can just reverse his EM Shield? Well, you just answered the question, because she can manipulate EM Energy.
Reverse polarity will cause a large decrease of Magneto's field strength making it weak. Or it can create a potential shock hazard. Now, magnetic fields don't represent a shock hazard but electric Fields do. And like an electric field, a magnetic field produces electric current and if a magnetic field changes it creates an electric field.
Storm has electrokinetic abilities so she has the option of weakening Magneto's magnetic field or frying his ass and burning him at the stake with his own powers. Magneto is not immune to voltage. That's how reverse polarity works. But if you're asking how Storm can nullify Magneto's magnetic field she can generate an equal magnetic field going in the opposite direction of the first current.
People always seem to think that Lightning doesn't harm Magneto, it makes him Stronger. And they always use this scan here where Magneto says: "Lightning "strikes" make me stronger." But they take that out of context. It's not the voltage that makes Magneto stronger; it's the current. Because lightning strikes are rapidly moving electric currents and the movement of electric charges produces a magnetic field. That's why he says lightning strikes makes me stronger.