The quick answer is that: No, nutritional yeast is not bad for you.
In fact, it’s quite healthy, especially if you’re a vegan.
It has loads of pretty much all B-Vitamins: thiamin, riboflavin, niacin, B6, folate, and B12. It’s one of the best food sources of B12 for vegans. If you’re not going to use a vitamin B12 supplement as a vegan, you should be eating nutritional yeast regularly.
There’s nothing in it that would hurt you unless you’re specifically allergic to it.
While it’s possible to eat too much nutritional yeast, you’d have to eat multiple cups per day, which seems very difficult.