Modeling water may indeed be an issue for photogrammetry.
The problem with images which capture only water is that they cannot be calibrated.
This happens because it is very hard to find and match characteristic points on water surfaces, since these points are not stable (water moves, sun reflects, surface is homogeneous).
This issue regarding finding key points and matching them between images also applies to NIR and thermal datasets. If the pixel values are too similar Pix4Dmapper will not be able to detect key points. It mostly depends on patterns of the water surface and if the fluctuations are captured by the camera.
Images that contain only water will not be calibrated and so will not contribute at all to the processing. Consequently they can not be used to derive a 3D model. To reconstruct other water surfaces such as rivers or lakes, each image needs to have land features. Flying higher may help to include more land features