### 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)

Ref<SceneState> ss;
	if (p_node == p_root) {
		ss = p_node->get_scene_inherited_state();
	} else if (!p_node->get_scene_file_path().is_empty()) {
		ss = p_node->get_scene_instance_state();
	}
	if (ss.is_valid()) {
		String path = ss->get_path();
		if (!checked_paths.has(path)) {
			uint64_t modified_time = FileAccess::get_modified_time(path);
			if (modified_time != ss->get_last_modified_time()) {
				return true; 
			}
			checked_paths.insert(path);
		}
	}
	for (int i = 0; i < p_node->get_child_count(); i++) {
		bool found = _find_updated_instances(p_root, p_node->get_child(i), checked_paths);
		if (found) {
			return true;
		}
	}
	return false;
}
bool EditorData::check_and_update_scene(int p_idx) {