I would agree that the problem decreases with the popularity and recency of the book. If you're talking about a newly published bestseller, which is what I imagine most people buy, your chances of running across a fake are pretty small in my experience.

I would be afraid that this could change that, though - especially when e-book editions are released concurrently, it takes only a modicum of effort for a scammer to pirate the book and produce a realistic looking fake. (The advantage here, I suppose, is at least the presence of an official e-book means a professionally edited fake, rather than what you tend to see for out-of-print/old books.) Part of what makes that experience so much smoother is generally speaking, right now, if you go search for a new and/or very popular book, you'll be buying from the publisher or from Amazon.

How would you know that you didn't receive a counterfeit​?

If I can't tell the difference, does it matter to me?