Their stock price was low but their balance sheet was solid. Nintendo was doing just fine even with the poor performance of the Wii U. The DS was still making bank for them. They were never under threat of going the route of Sega.
The balance sheet was admittedly solid, Nintendo is a conservative company and always makes it a point to stay in the black (I think the Wii U was the first console they sold at an initial loss EVER). But while the 3DS did decent, it did not do even close to the numbers put up by the DS. Don't let nostalgia shade your glasses:
Nintendo president says 3DS momentum is 'not so good' in US and Europe
That was Iwata acknowledging the 3DS underperforming 6 months prior to the Wii U dropping..and really bringing the house down
I remember all of this very vividly because I had some finances were closely tied to Nintendo, like $2K with them. I actually sold off most of it when Pokemon Go spiked their share price (a decision I regret, now I only have 6 or 7 shares or something).
Would the situation have been as dire as Sega after the Dreamcast? Probably not, maybe that comparison was a little much, but two failed hardware runs in a row would've backed even the GOAT into a tight corner, that much we all should be able to agree on.