I tried making a scene with all the shaders used as materials, then load it into the scene, then free it...

func do_shader_preload():
	game.shaders_preloaded = true
	var shaders = load("res://scenes/shader-preloads.tscn").instantiate()
	add_child(shaders)
	shaders.call_deferred("queue_free")

But it doesn't help. And the game stutter is worse in latest 4.1 dev, than in 4.0.X...

Turns out it is working now in 4.1-dev2!

Not 100% sure thats why, but whatever