We present secondary electron (SE) emission results from freely supported carbon/silicon nitride (Si3N4) hybrid nanowires using scanning electron microscopy. We found that, contrary to bulk materials, the SE emission from insulating or electrically isolated metallic nanowires is strongly suppressed by the penetrating beam. A mechanism of the SE suppression by the positive specimen charging is proposed, which is based on a total emission yield calculation using the Monte Carlo technique. This finding provides an important basis for studying low-energy electron emission from nanostructures under a penetrating electron beam.