Re: "Flat" design DOES NOT MEAN links aren't in a contrasting color. Or not in all caps.
If you read the linked article, the researchers talk about signifiers, and comment that "weak or absent signifiers" cause the problem. They also assert that flat designs tend to have a lot of weak or absent signifiers, and while they didn't attempt to prove that in the paper, I agree with them. Often the "hamburger menu" button at the top of webpages has no button-border (so the only signifier is the icon itself, hence weak) and even the search function is an unmarked clickable textarea (absent signifier) made worse by the fact that in some UIs you have to click in the text area, in other you can click in the text area or on the magnifying glass, and others still, you have to click the magnifying glass. Stronger signifiers makes this inconsistency less problematic.
Yes, flat design doesn't mean no signifiers, and 3D design doesn't always mean strong signifiers; but flat design biases away from strong signification, and pseudo-3D design biases towards strong signifiers. (Whereas true 3D design often eschews "signifiers" altogether and relies on stupid "object manipulation".