Summary:

Clickable UI elements with absent or weak visual signifiers condition users over time to click and hover uncertainly across pages—reducing efficiency and increasing reliance on contextual cues and immediate click feedback. Young adult users may be better at perceiving subtle clickability clues, but they don’t enjoy click uncertainty any more than other age groups.

BAD Flat Design. The same points could be made for skeuomorphism or any other trend. If your system is bad, your users will be less efficient. Lets not forget everything else on a product, because that's how a user determines if something is clickable. Users learn through CRAP (contrast, repetition, alignment, proximity). If your text is black and all of your links are black, then that's bad design. At the end of the day, not matter the style, bad design is bad design.

EDIT Also, please take a look at the footer of this website. The irony is too good.

I feel this way a lot of time. Design is not aesthetic!