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Can nutritional yeast flakes be used as a bread leavening, or is the yeast really dead (is that what deactivated means?)?

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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.

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    Is nutritional yeast the same thing as bread yeast at all? If it is brewer's yeast or some other kind, that's possibly worth mentioning. – rumtscho Jan 28 '16 at 20:31
  • Understanding that they are different, it's it's dead does that make much difference which strain of yeast it was? – Escoce Jan 28 '16 at 20:34
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    @rumtscho Wikipedia says it's usually S. cerevisiae, which is the same.... but there's a lot of varieties covered in that, so... who knows. – Catija Jan 28 '16 at 20:34
  • @rumtscho well, it's all strains of s. cervisiae and before commercial production of bakers'yeast started, bakers got their yeast from the brewers, simply skimmed off their large vats. Only when the brewers switched to cold-fermenting lager strains of s. carlsbergiensis (or s. pastorianus), bakers yeast (still s. crevisiae) was cultivated explicitly for baking. Note that "cervisiae" hints to the origin as "beer", but is misleading here. – Stephie Jan 28 '16 at 20:37
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    @Geremia No, it's dead, nothing you can do about it. Instant/dry yeast contains dormant but live cells; when you add water they go from dormant to active, not dead to alive. – Cascabel Jan 29 '16 at 0:18
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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.

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