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...