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Looking at the nearest thing I have to a decent reference on style (the Canadian Style) on footnotes/endnotes/citations/etc., the recommendation is to use a superscripted number which can be between brackets or parantheses which are also superscripted.
An alternate is to use a symbol which is unique within a page and/or chapter ( *, †, ‡, §, ‖, ¶, etc.). Though these days, no one uses the traditional squared 4 dot punctuation mark ⸬ which looks rather like a double colon.
Given that footnotes do not exist as such in a ebook and are often collected in a single file as endnotes, I prefer to use unique superscripted numbers within square brackets just to make them larger and easier to touch and easier for me to locate when editing.
Of course, this runs into fun when a single endnote may be referenced from multiple locations and you do not have popups for the notes or a note links to another note.
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