Hi Mo,
the Nikuradse roughness can be chosen independently of the water depth. So you can choose the same value for low water or high water. The value describes directly the roughness, has a physical unit (m) and can be derived from grain sizes (typically 3*d50 for skin friction).
For Strickler or Manning you have to adapt the value for different water depths.
Therefore, I prefer using Nikuradse. My experience is if you know the geometry precisely (e.g. lab model) and you have no form roughness (no dunes) 3*d50 will give a very good guess and you can predict the water levels (low water, mean water, high water) very well with the same Nikuradse roughness coefficient.
Best regards,
Rebekka