The Google page layout algorithm/penalty which originally launched in 2012 and has been updated a few times since is still an important algorithm says Google's Gary Illyes.
Gary was asked about it on Twitter and said, "yes, it's still important." I think the question came up because of the Fred update and what is appears to target. But Fred is more than just ads, in fact, not all sites hit by Fred had ads in the "bad spots."
That being said, Google does run the page layout algorithm automatically and yes, it is still something that can hurt you says Google.
So be careful with your ad placements - if you care about your Google rankings.
Forum discussion at Twitter.