What is the risk of food poisoning when making nattō
Your question has two facets. 

I’ll answer the first one. While brewing beer or wine as well, you’re advised to sterilize all the equipment and use a specific culture of bacteria. The reason for that is, if the “stuff” you’re trying to ferment gets some wild yeast/mold/bacteria, your end results won’t be what you desire. So you’re trying to minimize that risk by sterilizing it.

I believe people with relevant food-safety experince will better answer your second question on safety of fermentation. As I will leave it unanswered. Even though I also think in similar terms with you.