Living in borderline survivable conditions makes the body much more susceptible to infection. Add to that a virtually non-existent medical system and people are going to be overall less healthy. Using "night soil" is likely low on the list of causes for higher infection rates in North Korea.

Comparing the health of North Koreans and South Koreans is not a fare comparison. One nation has medical infrastructure, a good food supply, and a functioning economy. The other is a black hole with people regularly starving, no legal economy, and medical care only for the politically connected.