Lethn I've been doing some research and I don't know if the navigation server is meant to handle that many agents. What I did find however is that there is a concept called flowfield or vector fields in which you create a grid in which you calculate all shortest path to your target from all the squares on the grid and then you basically assign a vector to it. Once a unit is on a certain square, it does not have to calculate the next path, it only has to move in the direction of the precalculated vector. I am currently trying to figure out how to implement it but I'm far from being an expert at coding.
I did see videos of unity nav mesh system handling many agents and still having good performances so I'm not quite ready to give up on the Godot navigation system just yet, but knowing Godot is still early in its development I'm afraid that the performance I'm looking for might not be achievable with the navmesh system in the near future, even with threading. Not even sure if flowfields can do it either to be honest. Maybe GDScript is too slow for this kind of thing and we have to create a GDExtension to take care of it.
My specs are:
CPU: Intel i5-12600k
RAM: 32 GB