The query string parameter is used for "cache-busting" - when you've updated Q2A and the file changed, it shows as a different URL so that visitors get the new URL. I'm not sure why proxy caching servers would have problems with this as browsers handle it just fine and will cache the URLs if the appropriate Expires/Cache-control headers are set.
Anyway I don't think that issue would affect many visitors in reality and "fixing" it in core would cause more problems and hassle (e.g. having to rename all the JS files every time they changed). And some files like qa-styles.css cannot be changed as Q2A needs to look for that specific filename to determine which themes are installed.
If you really want to change it, it would be possible using a theme override of head_script(). You'll need to check each line for a script tag and do a str_replace/preg_replace on the URL.
