Is Nattou safe to eat when it has white dots on it?
Yes, those spots are normal, they form as the nattou ages. They are amino acid crystals, and they are perfectly safe. Here's a picture.



They're a bit crunchy, which you may or may not like. If you don't like the dots, get young nattou and consume it before the crystals form. If you do like them, get more mature nattou. With younger nattou, you should be able to store it opened in the fridge for a few days before the crystals start to form. As you have experienced though, once they start, they grow quickly.