### 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_sandboxed_renderer_client.cc
return render_frame->GetWebFrame()->GetDocument().Url().ProtocolIs(
      "devtools");
}
bool IsDevToolsExtension(content::RenderFrame* render_frame) {
  return render_frame->GetWebFrame()->GetDocument().Url().ProtocolIs(
      "chrome-extension");
}
v8::Local<v8::Object> GetModuleCache(v8::Isolate* isolate) {
  auto context = isolate->GetCurrentContext();
  mate::Dictionary global(isolate, context->Global());
  v8::Local<v8::Value> cache;
  if (!global.GetHidden(kModuleCacheKey, &cache)) {
    cache = v8::Object::New(isolate);
    global.SetHidden(kModuleCacheKey, cache);
  }
  return cache->ToObject(context).ToLocalChecked();
}
v8::Local<v8::Value> GetBinding(v8::Isolate* isolate,