In my previous experience a server specific bundle was always the better decision in the long run. I think you should try to keep your client- and server-code as close as possible.
If you don't want to compile your entire server code with webpack, you can also think about splitting your app into a presentation layer and a data layer. The presentation layer will always be bundled with webpack, the data layer is just a separate node.js application which does not know anything about HTML and CSS. It just returns JSONs.
That's probably also a good separation of concerns :)