### Godot version

Godot 4.1-beta2

### System information

Manjaro Gnome, Intel Core i7-11800H

### Issue description

On a relatively modern laptop (Intel Core i7-11800H), in a scene with many scripted nodes (total of 900+ with roughly half of them scripted), adding or duplicating a node freezes the editor for several seconds. Godot 4.0.2 handles such scenes much better!

Here is a flame graph captured while repeatedly duplicating simple Marker2D nodes with Ctrl+D in a complicated scene:
![Screenshot from 2023-06-15 23-54-38](https://github.com/godotengine/godot/assets/2766569/d0019f17-9b82-4a26-9b47-71fa7a3bef3a)

Performance data file to use with hotspot v1.4.1 (relevant data starts at the 75-second mark and lasts about 20+ seconds):
[perf.data.perfparser.zip](https://github.com/godotengine/godot/files/11763700/perf.data.perfparser.zip)



### Steps to reproduce

1) Add 1000 nodes with a script attached.
2) Duplicate a node and witness lags.

Also affects scrolling the scene tree dock.

### Minimal reproduction project

[add_node_lags_repro.zip](https://github.com/godotengine/godot/files/11763731/add_node_lags_repro.zip)

ERR_FAIL_INDEX_V(p_idx, edited_scene.size(), false);
	if (!edited_scene[p_idx].root) {
		return false;
	}
	HashSet<String> checked_scenes;
	bool must_reload = _find_updated_instances(edited_scene[p_idx].root, edited_scene[p_idx].root, checked_scenes);
	if (must_reload) {
		Ref<PackedScene> pscene;
		pscene.instantiate();
		EditorProgress ep("update_scene", TTR("Updating Scene"), 2);
		ep.step(TTR("Storing local changes..."), 0);
		
		Error err = pscene->pack(edited_scene[p_idx].root);
		ERR_FAIL_COND_V(err != OK, false);
		ep.step(TTR("Updating scene..."), 1);
		Node *new_scene = pscene->instantiate(PackedScene::GEN_EDIT_STATE_MAIN);
		ERR_FAIL_COND_V(!new_scene, false);
		
		List<Node *> new_selection;