I updated the list. I’m sorry - Stardew Valley is not unity, and “Nintendo” wasn’t specific enough to referring to some of their Pokémon projects. (I also added everything after “Pokémon” in the list after this comment and they all use Unity.)
Nintendo has used Unity for certain titles. Off the top of my head I can think of the Pokemon Sinnoh remakes, Super Mario Run, I think the fire emblem mobile game too?