Indeed. I don't know whether this is correct, but I'm sure I too heard that the park get fined if they release dyed water out of the Nemesis system into local watercourses, and that in the past this has happened both out of necessity when a lot of rain has fallen (obviously if the pit fills too much there's insufficient clearance between the water and the train when at the bottom of the loop for the ride to run) and by accident. The straw that broke the camel's back was when it happened several times in a row during a period of heavy rainfall, resulting in multiple fines and the decision to not put it in at all to avoid the expense and possible harm to the environment.
I have also heard (again not sure on the accuracy) that there's something that could be added to get rid of the dye when the water level needs to be reduced, but I guess doing that could take time that the park might not have when they need to get the ride running.
My personal view is that it's not much of a loss. I know Nemesis is meant to be an alien, and therefore it could plausibly have a circulatory system that works differently to ours, but in my mind the water always looked far too pink to be believable blood. The waterfalls look plenty good enough as they are, especially the spectacular one underneath the first stall turn.