After reading and editing a couple books with footnotes/endnotes, here are my observations:
By having the footnote at the end of the chapter, the ereader doesn't have to open a new HTML file when you refer to the footnote, thus going back-and-forth from the footnote and text is faster than with endnotes (and I would assume uses up less power on the ereader).
With footnotes that span multiple pages on the ereader, an additional link at the end of the footnote referring back to the text is very welcome.
Since endnotes are located at the end of the book, rather than the end of the chapter, reading from chapter to chapter is seamless. With footnotes, one might have to scan past several pages of footnotes to go to the next chapter. Of course this could be alleviated by inserting a 'Next Chapter' link before the footnotes.
Creating links manually in HTML is T E D I O U S. If the Sigil creators need ideas for implementation of anchors and links, I would heartily recommend taking a look at how Google Docs does it (they call anchors 'bookmarks' and insert a cute bookmark icon in place).