If there are more than 1000 references on a page (for example, the current version of the COVID-19 pandemic article, the superscripts will have thousands separators. However, the reference list at the bottom does not have the thousands separator.
In my opinion, the thousands separators don't add to the readability of the superscripts, and they should be removed. This is probably also the easiest solution technically, because there doesn't seem to be an easy way to tell browsers to format a HTML list with thousands separators (and there could be localization issues, where the client-side localization might use another thousands separator than the server-side localization that's currently used).