Just because it's mentioned in an in-game book doesn't mean it will be in the game. It's possible that the content of the book is not accurate in this regard, whether it was never correct to begin with, or it was rendered incorrect due to that part being retconned from the lore. And even if it is true in the lore that there are shrines dedicated to a lesser Daedra named Vernaccus, that doesn't mean the game will reflect this, after all, ultimately, what any game shows is not exactly like what it's province is like in the lore, but just a representation of it, it may be that some aspects will differ from lore, or some things in lore won't be in the game, not just in terms of scale (Obviously, Cyrodiil in lore is larger than it is in game.) but in terms of the overall content as a whole, so just because something is in the lore doesn't mean it will be in Skyrim.
Though I really don't see any reason to doubt there will be Daedric shrines in Skyrim in some form or another, when, since Daedra were created, has there been a main game in the series where they have NOT played a role? And Todd even pretty much confirmed there were Daedric quests in an interview, admitably, he just said the quests are there in some form or another, not that we'll get them from shrines, but I think we can assume we do get them from shrines, because that's easier to do than needing to actually summon the princes themselves, still, I think we'll only see the major Daedric Princes represented, lesser Daedra will only be enemies and summons, at most, we might get a few unique Daedra as NPCs, but I certainly doubt we'll see any shrines dedicated to Daedra other than the 16 Princes who had shrines in Oblivion (I know Mehrunes Dagon didn't have a quest in Oblivion, but I still think he counts as having a shrine due to the Mythic Dawn shrine, you just couldn't get a quest from it, which is understandable since Mehrunes Dagon is your enemy. It would confuse things somewhat if you try to help the Daedra you're supposed to be opposing.), no lesser Daedra.
Only the major Daedra are worshiped in shrines across Skyrim, and I wouldn't even know how they could implement that smoothly since most Nords don't worship those
I also don't recall most Imperials worshipping Daedra, yet there were Daedric shrines in Cyrodiil, and in Morrowind, worshipping the "bad Daedra" is actually illegal, and yet people still do it. Just because Daedra worship isn't considered normal in society doesn't mean it won't play a part in the game.