But this is for jQuery Mobile, and you don't get mouse hovers on the devices this is targeted for.
Many UI concepts are in flux (again). Link? Button? Collapsible? Let go of what you know and watch people using flat UI.
There are many ways to hint interactions within flat design. As has always been, stick to more abstract interaction fundamentals and processes and don't wed yourself to fads based on current (or old) tooling trends.
It's easy enough to use color, contrast, font, positioning, size, shape, etc. all to indicate interaction points. That's all a gradient button is compared to the text in an old message box.
Also, there are two major thrusts in flat ui that make it compelling. One is the additional focus on content since the UI takes a step back once you spend less time tweaking artificial details. Which leads into the second point others are making. The time and energy spent in details to achieve fake results in a digital context are dishonest at best and grossly out of place from a design perspective. There's a little bit for everyone in there.
"Flat UI is bad for usability" keeps getting repeated as a criticism against the flat UI trend but is not actually true.
Bad UI design is bad for usability, regardless of VISUAL style.
As jack_trades mentions, there are MANY other ways to convey interactivity without artificial depth, texture.
Think about a simple modal. Users know to look at the top-right, sometimes left, for controls for the modal. What difference does it make if the user sees a flat X icon or an X inside a beveled, drop-shadowed button?
Re: desktop vs. mobile; If a user has to hover over an element just to know if it's interactive then perhaps the design has already failed.
Crux of argument can be found in the statement: "Even lighting effects like drop shadows, form shadows, specular highlights, and reflections are dishonest because there’s no light source inside a digital screen that’s manufacturing these lighting effects." The article then puts forward the position that honesty to material creates more timeless design.
If your application is a music player, then having anything but a stereo knob to control volume is dishonest. Yes, it is not a hi-fi component made of steel. But you are making a music player. If it doesn't look and feel like a music player, you are dishonest.
The same argument can be used to relate to some of the most basic UI metaphors. A desktop is not a physical desktop. But users would prefer a visual layout of icons representing apps on their mobiles and computers than a list of app names to choose from. A window is not a physical window, either.
So while flash is bad, denying the role of metaphors is just as bad. Maybe worse.