As Luciano correctly mentioned, photogrametric software can not deal with water. Water is homogeneous and it´s hard to find common points on the images. In addition to this, water moves. Photogrammetry can not deal with moving points/objects.
As alreday mentioned, the best solution is to use the orthomosaic and/or the 3D Textured Mesh as they will have no holes.
@Dennis: You can erase the noise of the point cloud using our editing tools: https://support.pix4d.com/hc/en-us/articles/202560499
The deleted points will not be taken into account for the Mesh generation.
I have added your idea about the surface to our Suggestion list. Our Product Development Team will consider it for future version of the software.