Unmanned Aerial Vehicles (UAVs) are increasingly deployed across diverse domains and many applications demand a high degree of automation, supported by reliable Conflict Detection and Resolution (CD&R) and Collision Avoidance (CA) systems. At the same time, public mistrust, safety and privacy concerns, the presence of uncooperative airspace users, and rising traffic density are driving a shift toward decentralized concepts such as free flight, in which each actor is responsible for its own safe trajectory. This survey reviews CD&R and CA methods with a particular focus on decentralized automation and encounters with noncooperative intruders. It analyzes classical rule-based approaches and their limitations, then examines Machine Learning (ML)–based techniques that aim to improve adaptability in complex environments. Building on recent regulatory discussions, it further considers how requirements for trust, transparency, explainability, and interpretability evolve with the degree of human oversight and autonomy, addressing gaps left by prior surveys.