Yes. DF would see duplicate frames and count them as FPS. DF doesn't differentiate between the causes of lower framerates, whether rendering or game physics, and it doesn't make a difference really. Although I'm certain if they came across a physics slowdown in any game they tackle, they'll report it, because it's extremely rare these days. TBH I'm not surprised it's Nintendo showing the problem in this day and age - it's suitably retro an approach for them.
Any and every game dev is well informed about decoupled physics and rendering, and delta times for smooth updates. The major middlewares handle a lot of this pretty transparently too.
Edit - is the slowdown smooth on Wii U, or does it notably drop frames? Rendering could still be decoupled an tweened for delta time. That'd show as 60fps, and rightly so, even though the game physics drops to 30 fps.