Reverse Polarity Protection for DAQ box
You said you are going to use a 50 mV shunt with a 34 V, 16 bit ADC. My first comment is that because the shunt output range is such a small portion of the ADC range, you will not get much resolution in your readings.

But specific to your question, the specs for your Omega ADC says that it can measure down to -2 volts. So when the polarity reverses on your shunt, the -50 mV is still well within the range of the ADC converter. You should not have a problem.