What should be the sampling frequency for a square pulse train in a DAQ system?
Assumption: The pulse timing and frequency are desired as input, not the actual waveform.

If the pulse train is known to be essentially just pulses, i.e. with nearly vertical rising and falling edges, then an analog waveform acquisition mechanism is sub-optimal.  

Greater precision would be obtained by using a comparator or a Schmitt trigger, sending its output to a GPIO, and using interrupts on the GPIO to capture the rising and falling transitions against a high precision timer.

To avoid false triggering in case the pulse stream edges are noisy, use a comparator with a fair bit of hysteresis. That way, brief noise pulses on the rising and falling edges will not falsely trigger the GPIO interrupts.