FFT Result - which bins are useful
I believe you should use the Nyquist bin every time. By having it, you can always recreate the full DFT of your real-valued signal from the first half of spectrum. Whereas if you discard this value there is no way back and you can recreate your time domain signal. 

As in answer you pointed to, usually the Nyquist bin shouldn't contain any data when while using anti-aliasing filter. Nevertheless sometimes you might want to estimate the energy of your signal from it's DFT. You might therefore get inaccurate value. Question is, do you really care about such accuracy?

Just to wrap up. I always use Nyquist bin and I don't need to ask myself these questions.