http://tsubakit1.hateblo.jp/entry/2017/04/28/005237 の処理改良版(プレハブがプレハブ参照のまま複製可能)

ObjectDeplicate

using UnityEngine;
using UnityEditor;
using System.Linq;

public class ObjectDeplicate {
	[MenuItem("Edit/DummyDeplicate %d", false, -1)]
	static void CreateEmptyObject() {
		var select = Selection.objects;

		// Projectのオブジェクトのコピー
		var project = Selection.objects.Where(obj => AssetDatabase.GetAssetPath(obj) != string.Empty);
		foreach (var obj in project) {
			string path = AssetDatabase.GetAssetPath(obj);
			var newPath = AssetDatabase.GenerateUniqueAssetPath(path);
			AssetDatabase.CopyAsset(path, newPath);
		}

		// ヒエラルキーのコピー
		var prefab = Selection.objects.Except(project).Except(scene).ToArray();
		foreach (var obj in prefab) {
			// Selection.activeObjectなど単体での差し替えでは切り替わらない
			Selection.objects = new GameObject[] { obj as GameObject };
			Unsupported.DuplicateGameObjectsUsingPasteboard();
			// ここで参照がコピー先に切り替わる
			var gameObject = Selection.objects[0] as GameObject;
			int start = gameObject.name.LastIndexOf(" (");
			gameObject.name = gameObject.name.Substring(0, start);
			gameObject.transform.SetSiblingIndex((obj as GameObject).transform.GetSiblingIndex() + 1);
			Undo.RegisterCreatedObjectUndo(gameObject, "deplicate");
		}
	}
}