You know, the obtuse interface and ASCII graphics of Dwarf Fortress don't bother me but they do hold me back from recommending it. I grew up on the Ultima series, MUDs and old-school roguelikes so my standards here are a bit dated. For a kid growing up in the age of Dark Souls III, a game like Dwarf Fortress might be relentlessly difficult to get into.
[1] http://www.pcgamesn.com/indie/physics-teacher-blasts-his-stu...
Its a fun game, but not that kid friendly IMO.
KSP and Factorio are both better options.
Dwarf Fortress is fun, but different. It feels more like a narrative generator to me.
Edit: unsure why this is downvoted. People don't 'graduate' to games, each one appeals to people for different reasons. If you want your kids to play a more educational game, minecraft with mods is that game.
Gnomoria is already quite advanced (mechanically) and has been getting content updates for ages.