Few epubs have toc
 

That's a subjective conclusion. I keep noticing a message saying something like "This book does not have a table of contents."

Now since some at least of the books for which this comes up have a page listing all the chapters, I assume that a toc in the sense of the error message is something other than a list of chapters, maybe a way to jump quickly to a given chapter, like the clickable page numbers in some pdfs.

So what's the received wisdom? Should one put in a toc in an epub?

Now I'll post this and probably find that six other people have asked the same question, although I couldn't find it with the search function. <sigh>

The ePub standard includes a toc.ncx file where the TOC is specified. So far as I know, all ePub readers support toc.ncx and it really is the best way to do an ePub TOC. The exception is if the headings include any non-Latin characters, because badly implemented ePub Readers (and in particular Adobe Digital Editions, as used on most E Ink devices) use a system font for the TOC with poor glyph coverage.

An in-line TOC, i.e. a set of hyperlinks in the body of the text, is better than nothing, but inferior to a real TOC. I agree that in-line TOCs are quite common as are ePubs with no usable TOC of any kind.