Can nutritional yeast flakes be used as a bread leavening, or is the yeast really dead (is that what deactivated means?)?
Well, your own link states clearly:
When the yeast is ready, it is killed (deactivated) with heat and then harvested, washed, dried and packaged.
So no, you can not use nutritional yeast to leaven your dough.
Only live yeast manages to create CO2 bubbles as byproduct of its digestion. Many novice or careless bakers inadvertantly kill their yeast by using too-warm liquid - and end up with a dough that never rises.
Nutritional yeast is commonly used in unholy amounts as a seasoning in seitan - which is an ultra-high gluten dough that, while it needs some force to leaven, is annoyingly good at trapping gas. Steam leavening alone can already become a problem. And luckily: The nutritional yeast does not leaven it.
So: Doesn't leaven anything, QED.