I have noticed a few discussions regarding this question.
It would seem that we all have our personal preferences. So this is a "general" opinion from someone who has been in the commercial typesetting trade for over 40 years.
On the paper product. Should be at the foot of the page where the footnote explains/expands an idea or word expressed on that page, usually with an asterisk, dagger, double-dagger, etc. The readers eye can quickly access that information, and aids the reading experience. On Ebooks, in my humble opinion, this type of footnote could easily be inserted into the text using, say brackets "[ ]" or parenthesis "( )" so long as they are not overly long expansions, then it would become obtrusive. Longer explanations could be put at the end of the paragraph on which they appear, perhaps using the asterisk, etc. model, but not "clickable". After the first use of this convention the reader would very quickly realise this is the way footnotes have been treated on their Ebook. Unless the reader is extremely fussy, both practices mentioned above, would not be overly obtrusive and should not detract from the reading experience.
This type of note will contain academic information such as, publication, date, publisher and folio, to which that piece of text refers, perhaps a quote or an idea expressed from that publication. Researchers would want to access this type of information in the course of their investigations. So on the Ebook it should be made clickable. For the general reading experience, though, it is not necessary to have this type of note "to hand". If this type of note has an expanded explanation of the text being referenced, then in my opinion the note/text is not well written.
This argument will rage for years. Academes, by their very nature, will want to have a "weighty" academic looking book in their hands. But Kindle's all look the same, mostly, whether your reading a novel or getting your head round the intricacies of rocket science.
To sum up: Ebooks are in their infancy . . . "What!" You may say. "I've been doing ebooks for years!" We'll, with reference to the paper/papyrus product, they very much are, I'm afraid. Author's and publishers will need a new set of conventions regarding ebooks, not just cobbling the paper product into an electronic format.
Just to reiterate, this is my humble opinion and is a very general stroke of the brush. Make of it what you will.