Godot's head developer admits that if you want to do anything performance-intensive (e.g. thousands of interacting entities, AAA stuff) with Godot, you will likely end up hacking the low-level engine code or even using a separate ECS/DoD implementation. At that point, why not use a proper ECS engine?
https://godotengine.org/article/why-isnt-godot-ecs-based-gam... (see "Optimization" section and below)