I think best solution is to put the hashed js file name in require definition, not the original clear name.
You can echo the hashed name using the resource external tag
<r:external uri="js/custom.js"/>
<script type="text/javascript">
var urlOfCSSToLoadInJSCode = '${r.external(uri:"css/custom.css").encodeAsJavaScript()}';
</script>
<r:external uri="icons/favicon.ico"/>