When Craft generates a “resource URL” from a front-end request, it just takes whatever the current site URL is, adds the resourceTrigger config setting (“cpresources”), and then adds the path that was passed in (“smartmap/js/smartmap.js” for example).
So if your site URL is “/en”, then that’s going to be part of the resulting resource URL.
As long as there’s a working Craft index.php file at /en/index.php, and you’re able to serve regular front end pages from that base URL, then there’s no reason the “en/” part should be tripping anything up when serving resources.
All of the CP’s front-end resources are served through the same mechanism – try going to /en/admin (or whatever your cpTrigger is set to) and seeing if the CP is working normally from there.