Absolutely, the zapper can directly kill bacteria, protozoa, fungi, and other single celled microbes as well are only a few higher organisms such as rotifers and likely, certain crustaceans.
However, since certain higher organisms such as helminths are highly dependent on certain microbes such as wohlbachia sp. then it is possible to kill those helminths by killing the microbes that these worms are dependent on. In fact, that is exactly the mechanism that certain anti-helminthic drugs depend on for their effectiveness.
And since ParaZapper is demonstrably more effective at killing a wide range of the microbes than regular zappers, this makes ParaZapper the best choice for such efforts.