### 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
#include "third_party/blink/public/platform/web_isolated_world_info.h"
#include "third_party/blink/public/web/blink.h"
#include "third_party/blink/public/web/web_document.h"
#include "third_party/blink/public/web/web_draggable_region.h"
#include "third_party/blink/public/web/web_element.h"
#include "third_party/blink/public/web/web_local_frame.h"
#include "third_party/blink/public/web/web_script_source.h"
#include "ui/base/resource/resource_bundle.h"
namespace electron {
namespace {
base::StringPiece NetResourceProvider(int key) {
  if (key == IDR_DIR_HEADER_HTML) {
    base::StringPiece html_data =
        ui::ResourceBundle::GetSharedInstance().GetRawDataResource(
            IDR_DIR_HEADER_HTML);
    return html_data;
  }
  return base::StringPiece();
}
}  
AtomRenderFrameObserver::AtomRenderFrameObserver(
    content::RenderFrame* frame,
    RendererClientBase* renderer_client)
    : content::RenderFrameObserver(frame),
      render_frame_(frame),
      renderer_client_(renderer_client) {
  
  net::NetModule::SetResourceProvider(NetResourceProvider);
}
void AtomRenderFrameObserver::DidClearWindowObject() {