Catalysis of the reaction: NAD+ + 2-dehydro-3-deoxy-D-gluconate = NADH + (4S)-4,6-dihydroxy-2,5-dioxohexanoate.
2-keto-3-deoxy-D-gluconate (3-deoxy-D-glycero-2,5-hexodiulosonic acid) dehydrogenase activity