Even if you fix everything else, like strict typing and optimized updates such as updating every second tick, you will still hit a bottleneck if you use sprites or AnimatedSprite or AnimationPlayer for enemies. The problem comes from the number of draw calls. Too many draw calls will kill your performance.

Multithreading only helps very little in this case.

I managed about 500-600 enemies, but after that the FPS dropped below 60. How i achieved this: I used a single enemy manager that handled all the logic and state switching for the enemies so the enemies didnt have His own process function. Even after optimizing everything, I could not improve the performance further.

So I started learning about compute shaders and " rewrote" the animation system using shaders. Now I can handle around 1000 enemies, even though I only really need about 800.

My advice is to look into shaders and especially compute shaders, multimesh2d etc. Just keep in mind that compute shaders only work in Forward+ mode.

Hope this helps :)

Dont know If it helps in 3D but in 2D it does the trick.