In a funny way Nintendo themselves has actually kinda mismanaged their smartphone division. By not making Mario free to play and instead trying to force a pay model they kinda cut the legs off of it. Fire Emblem is doing OK, but Fire Emblem has no business out grossing Mario ... Mario is their top IP, Fire Emblem is like maybe no. 13? The Mii app did not take off at all.
The huge success for Nintendo in smart apps came with Pokemon GO, but that's something they really didn't have much involvement with, it's possible if they had designed the app, they would have screwed it up by putting it behind a pay wall or doing some other weird thing with it.
They were never in any real financial danger, their hardware market was probably in some trouble though. 3DS + Wii U after 5 years would have had maybe 80 million combined in sales ... that's significantly lower than GBA + GCN even (102 million there and GBA only had really 3 1/2 years on the market to itself).
