### 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
v8::Local<v8::String> key,
                                mate::Arguments* margs) {
  v8::Local<v8::Object> exports;
  std::string module_key = gin::V8ToString(isolate, key);
  mate::Dictionary cache(isolate, GetModuleCache(isolate));
  if (cache.Get(module_key.c_str(), &exports)) {
    return exports;
  }
  auto* mod = node::binding::get_linked_module(module_key.c_str());
  if (!mod) {
    char errmsg[1024];
    snprintf(errmsg, sizeof(errmsg), "No such module: %s", module_key.c_str());
    margs->ThrowError(errmsg);
    return exports;
  }
  exports = v8::Object::New(isolate);
  DCHECK_EQ(mod->nm_register_func, nullptr);
  DCHECK_NE(mod->nm_context_register_func, nullptr);
  mod->nm_context_register_func(exports, v8::Null(isolate),
                                isolate->GetCurrentContext(), mod->nm_priv);
  cache.Set(module_key.c_str(), exports);
  return exports;
}
v8::Local<v8::Value> CreatePreloadScript(v8::Isolate* isolate,
                                         v8::Local<v8::String> preloadSrc) {
  return RendererClientBase::RunScript(isolate->GetCurrentContext(),
                                       preloadSrc);
}
void InvokeHiddenCallback(v8::Handle<v8::Context> context,