I'm usually fairly cognizant of ligatures when I'm reading, but obviously I can only comment on the things I have read with my imperfect memory. The book I'm reading now (Harmonic Experience by Mathieu) is certainly what I would consider to be professionally typeset, and it does not use the "fi" ligature. Godel, Escher, Bach, on the other hand, does use it from what I remember. The Lifebox, The Sheashell, and the Soul does not use it (I just checked). From my memory, few of the physical novels I've read used it, but I'm not too confident in that memory because all of my novel reading has been done on a Kindle for several years (the portability and convenience won out over typography). I've read almost no physical newspapers or magazines since I was quite young, so you might be very correct about that.

It really comes down to who your audience is, and perhaps it's true that most things you would even consider using LaTeX for are intended for an audience savvy enough to not be distracted by ligatures.