How do ADC/DACs deal with out of sync signals near Nyquist frequency?
How does it faithfully recreate the waveform if the samples are taken a points that are 0?


Not at all. Things at $\frac{f_\text{sample}}2$ might just as well be constants. You can't tell [0 0 0 0] (sampled 24 kHz signal at zero-crossings) from [0 0 0 0] (sampled zero constant signal).

Nor can you tell [0.1 -0.1 0.1 -0.1] (sampled 24 kHz signal with amplitude 1 just a bit after each zero-crossing) from [0.1 -0.1 0.1 -0.1] (sampled 24 kHz signal of amplitude 0.1, sampled at its extrema!).

You need the sampling rate to be higher (not only just as high) than two times the highest signal frequency component for this to be unambiguous.