I'm not sure, but I don't think so. I mean as long as developers still put in as much effort into the handhelds as they do.
I don't see the "encroaching mobile market" as much of a threat if quality maintains its status quo right now. Actually good mobile games worth their money and not riddled with microtransactions are still diamonds in the rough. Ok, one has to compare the cost of them, 3DS games are pretty expensive, but I still don't see the ratio improving. Mobile are riddled with shovelware, with a business model that everyone wants to emulate first, and worry about producing something groundbreaking second. It seems purely based around money.
I don't see that changing any time soon. Although I've never been much of a handheld gamer myself, I am curious what the NX will do, and I doubt it would cannibalize it's own industry. Then again you never know.