### 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
const std::string& hidden_key,
                          const std::string& callback_name) {
  auto* isolate = context->GetIsolate();
  auto binding_key = mate::ConvertToV8(isolate, hidden_key)
                         ->ToString(context)
                         .ToLocalChecked();
  auto private_binding_key = v8::Private::ForApi(isolate, binding_key);
  auto global_object = context->Global();
  v8::Local<v8::Value> value;
  if (!global_object->GetPrivate(context, private_binding_key).ToLocal(&value))
    return;
  if (value.IsEmpty() || !value->IsObject())
    return;
  auto binding = value->ToObject(context).ToLocalChecked();
  auto callback_key = mate::ConvertToV8(isolate, callback_name)
                          ->ToString(context)
                          .ToLocalChecked();
  auto callback_value = binding->Get(context, callback_key).ToLocalChecked();
  DCHECK(callback_value->IsFunction());  
  auto callback = v8::Handle<v8::Function>::Cast(callback_value);
  ignore_result(callback->Call(context, binding, 0, nullptr));
}
}  
AtomSandboxedRendererClient::AtomSandboxedRendererClient() {
  
  NodeBindings::RegisterBuiltinModules();
  metrics_ = base::ProcessMetrics::CreateCurrentProcessMetrics();
}
AtomSandboxedRendererClient::~AtomSandboxedRendererClient() {}