My habit has been to check the first couple in a new book and see whether they are footnotes (of the explanatory aside type) or endnotes/citations. The former I will generally click on, the latter I might skim through at the end if I’m looking for additional material to read.

As you rightly point out, the real irritant is editors who merge the two types meaning that you have to click on everything just in case it’s a useful aside or explanation of a term. Simon Schama’s books suffer from this, 80% are simple citations but others contain useful additional context.

On Kindle (and I presume in ePub) you can use different marking schemes for footnotes and citations (e.g. * for a footnote, 1 for a reference) but it’s hit and miss whether publishers/editors make use of these.