I stand corrected, 9-volt zappers of the variety Hulda Clark describes in The Cure For All Diseases (the most common, easy to build kind) generally leave at least some of the bowel contents untouched. I checked the book and she does state that although the center of the bowel is often unaffected, sometimes it is nearly completely sterilized, and she recommends homemade yogurt and buttermilk to recolonize the bowel if this happens.
As to there being preferable frequencies, I'd be interested to see your research. If it's based on actual experimental results, I would certainly give it some weight. Variable-frequency zappers are based on a completely different principle than the Hulda Clark pulsed direct current zapper. They are useful for zapping certain kinds that have ways of hiding from the positive-offset zapper -- candida is one of these, according to TCFAD. But even these have to come out once in a while, and zapping gives the immune system a chance to recover and focus on them.
It seems like the whole resonance issue is a red herring when you try and apply it to positive-offset zappers which work at ANY frequency, with ANY waveform, at as low as 5 volts. Zapper manufacturers often boost the voltage to even out the square wave, but there's no scientific reason to do so -- it just looks good in their marketing materials and they use it to say (based on consumer misconceptions) that it makes their zapper better.