There is one solution for all of this that doesn’t involve query string. let’s say your module files are in /modules/. Use relative module resolution ./ or ../ when importing modules and then rewrite your paths in server side to include version number. Use something like /modules/x.x.x/ then rewrite path to /modules/. Now you can just have global version number for modules by including your first module with
<script type="module" src="https://stackoverflow.com/modules/1.1.2/foo.mjs"></script>
Or if you can’t rewrite paths, then just put files into folder /modules/version/ during development and rename version folder to version number and update path in script tag when you publish.