Nintendo and Microsoft have their own custom engines and toolchains for AAA games. Unity gets used for casual titles where teams are smaller, roles are less specialized, and high performance rendering isn't as big of a priority. (Not that Unity is slow, it's just behind the curve of Unreal and the custom engines of big studios)
The safe bet for Breath of the Wild is to assume that Nintendo used an in-house engine. Although it is public information that the dev team used a modified version of Havok as the principle physics engine.
