The Nemesis
Semper Tyrannus
My thought was more marketing dollars and shelf space. Carrying 3 consoles, related accessories, and Amiibos takes up a decent chunk of room. Nintendo just has a terrible time matching demand/striking when the iron is hot, even the new 3DS was OOS everywhere around Christmas, and depending on how similar the mini NES hardware is to the 3DS (both ARM based), it frees up components dropping the former.
And if/when the Switch adds its VC, having the mini NES around makes those $5 digital ROMs less attractive.
Otherwise, I agree they're targeting mostly different subsets of Nintendo gamers, the mini NES is more geared more towards the retro set (but I still contend a Pi is a just better all around option).
Except for that whole sticky issue of downloading ROMs to run on such a device being illegal.