I don't know about the long term effect of cleats on the knee, but people who wear them and play in sports where cutting is pivotal (like football or soccer) are at higher risk for ACL injuries
One of the factors believed to increase non-contact ACL injuries is the interaction between soccer shoes and the playing surface. In other words, cleats getting caught in the turf and poorly maintained fields can contribute to these injuries. Indoor soccer has a significantly higher rate of ACL injuries than outdoor soccer. It may be that the tendency of artificial turf to grab onto the shoes could lead to ACL injuries. In that case, the newer indoor surfaces, which appear not to catch players’ shoes so easily, may be safer surfaces for indoor play. More research is needed for definitive answers to these questions.