Indeed, you can. It's called "User style tweaks". Basically create something like "footnote.css" file in the styletweaks directory. Then you can go to the style menu and enable it for all books/specific book. Alternatively you can add per book styletweak from within KOReader, without creating any extra files. It works for one book though. See
https://github.com/koreader/koreader/wiki/Style-tweaks