The frequency and geographical distribution of filling henge ditches with water is unknown. In fact there is little evidence at all that the ditches were artificially filled with water. Rain and snow melt could provide the source of sediment in a ditch, or result in apparent erosion of the ditch walls as an indicator of water entering the ditch.
The idea of filling a henge with water as a means to observe the sky via reflection is the product of two historically unexplained issues related to the ditches. 1) Why were henge ditch and banks constructed, and 2) Is it possible the ditches aided observation of alignments extending from the henge to the horizon? The reason for excavating a henge ditch to the depth and width we observe today remains unanswered. However there should be no doubt as to why henge ditches are circular, and the purpose of the ditch/bank. Simply, the circle separates the profane beyond the circle from the sacred inside the circle. Constructing a circle to create such division was and remains a common means of delineating sacred space and the profane. If you have interest in this topic I suggest reading 'The Sacred Sphere: Exploring Sacred Concepts and Cosmic Consciousness through Universal symbolism." Admittedly I am author of the book, but there is no other publication that details the fact that virtually all ancient and indigenous cultures around the world and throughout time used the circle as a symbol of the sphere, and the sphere symbolizes the four sacred relationships between people, Earth, Cosmos and Creator, in all directions and at all scales throughout the universe.
As to the possibility of filling the ditches with water for the purpose of astronomical observation, this is an idea that has been explored but there is no evidence that it was applied in reality. It is possible that the sun, moon, planets or stars might be seen reflected by the water surface, but site conditions would need to be extremely favorable to ensure accurate observation. In sum I consider the idea to be little more than educated speculation lacking enough evidence to warrant further study, at least on my part.
Concerning use of advanced mathematics during prehistory, I argue that people have a natural tendency to observe the world spatially and not necessarily numerically. Constructing the 'Grand Design' across 8 square miles of the Stonehenge Sacred Landscape in about 3500 BC was most probably accomplished by applying little more that rudimentary surveying skills - turning angles at certain locations, and measuring distances between two points. The method was used by the Sumerians and ancient Chinese and Egyptians to construct wondrous landscapes including such structures as the pyramids a Giza. The methods are still used by surveyors today. Adding and subtracting is all the mathematical skill necessary.