I was going to suggest something similar what wideeyenow suggested, except that I don’t see any need to make something a MonoBehaviour if you don’t explicitly need to. The service that maintains the collection of relevant MonoBehaviour references, Master in wideeyenow’s example, could also be a pure C# class if you prefer.
When the MonoBehaviour or other components need to be referenced, they can register and deregister with some relevant service, either in Awake and OnDestroy, or OnEnable and OnDisable, depending on the intended design. Communication between classes and components can take place through those services, and it can be done with strong type dependencies, or it can all be loosely coupled. Interfaces and events help with loose coupling.
For example, all player MonoBehaviours could register with some relevant service when they are activated. The same could be true for all enemy related MonoBehaviours, and relevant other components or objects they reference. This could be one service that managers the players and enemies, or separate services that focus on one concern or the other. In addition to registering themselves centrally with a service, they can subscribe to observe events on that service, such as EnemyCreated, Enemy Destroyed, or PlayerAdded, PlayerRemoved. They could receive those events with the references to the relevant objects as event data, or they could get references to, for example, an AllEnemies list from that service as needed.
Abstracting some of these ideas far enough can leave you with a totally general purpose messaging system or something like it.
I saw a former military veteran in another thread describe it in similar terms to having a central command on the battlefield. If one unit needs to make decisions they relay information to central command, who has access to all of the necessary data for making bigger picture connections, and central command relays the relevant information back to the units.
However, there are so many different ways to tackle these kinds of issues, and without having detailed knowledge of exactly how your particular project is intended to work I can only offer a general opinion. Hopefully it helps inspire you toward a solution you enjoy.