It largely depends on how professional the person doing the conversion is. Most ebooks should be using typographic quotes these days, but there are still a few lazy publishers who don't check that the work's done properly.
An ePub can use any character you want, as long as the font has the right glyph to display it. Since you can embed your own fonts, it's perfectly possible to use ligatures as long as the type is set correctly.
Converting the quotation marks yourself is not easy. There's some discussion about it
here and
here I think if you search in the Workshop forum you'll find a few other threads, but can't locate them right now. The bottom line, though, is that you'd need to tear it down, edit, and then reconstruct the epub, since there aren't any simple conversion tools that I know of.