### Preflight Checklist
* [x] I have read the [Contributing Guidelines](https://github.com/electron/electron/blob/master/CONTRIBUTING.md) for this project.
* [x] I agree to follow the [Code of Conduct](https://github.com/electron/electron/blob/master/CODE_OF_CONDUCT.md) that this project adheres to.
* [x] I have searched the issue tracker for an issue that matches the one I want to file, without success.

### Issue Details

* **Electron Version:**
  5.0.1
* **Operating System:**
  windows
* **Last Known Working Electron version:**
  n/a

### Expected Behavior
A preload script should run only 1 time for each webContents / iframe

### Actual Behavior
The preload script appears to run multiple times

### To Reproduce
https://github.com/Tim91084/electron-node-subframe-issue/tree/node-in-subframe-runs-too-often

```sh
$ git clone https://github.com/Tim91084/electron-node-subframe-issue.git -b node-in-subframe-runs-too-often
$ npm install
$ npm start || electron .
```

### Screenshots
![image](https://user-images.githubusercontent.com/5086428/58273769-63b9d900-7d5f-11e9-8d30-1525dea34ce3.png)

shell/renderer/atom_render_frame_observer.cc
renderer_client_->DidClearWindowObject(render_frame_);
}
void AtomRenderFrameObserver::DidCreateScriptContext(
    v8::Handle<v8::Context> context,
    int world_id) {
  if (ShouldNotifyClient(world_id))
    renderer_client_->DidCreateScriptContext(context, render_frame_);
  bool use_context_isolation = renderer_client_->isolated_world();
  bool is_main_world = IsMainWorld(world_id);
  bool is_main_frame = render_frame_->IsMainFrame();
  bool is_not_opened = !render_frame_->GetWebFrame()->Opener();
  bool allow_node_in_sub_frames =
      base::CommandLine::ForCurrentProcess()->HasSwitch(
          switches::kNodeIntegrationInSubFrames);
  bool should_create_isolated_context =
      use_context_isolation && is_main_world &&
      (is_main_frame || allow_node_in_sub_frames) && is_not_opened;
  if (should_create_isolated_context) {
    CreateIsolatedWorldContext();
    renderer_client_->SetupMainWorldOverrides(context, render_frame_);
  }
  if (world_id >= World::ISOLATED_WORLD_EXTENSIONS &&
      world_id <= World::ISOLATED_WORLD_EXTENSIONS_END) {
    renderer_client_->SetupExtensionWorldOverrides(context, render_frame_,
                                                   world_id);
  }
}
void AtomRenderFrameObserver::DraggableRegionsChanged() {