Signal Tap Problem: Some signals have jitter

In a SignalTap set-up the same clock that generates the signals is used to sample these signals. The resulting waveform will then resemble what you would see in a simulation waveform. This has nothing to do with sampling as described by Nyquist-Shannon. BTW if you want to apply this to a 100 MHz square wave signal you would need a far higher clock as you have to cover twice the bandwidth of the signal, think of the bandwidth needed for an oscilloscope to display this 100 MHz signal.