It's a variation on the common expression "like two peas in a pod," meaning two people who are very similar to each other, especially if they share a physical resemblance. So when Mama Buki says that Sade and Papa are like two beans from the same pod, that's what she means.

When she brings them both a drink at five o'clock in the afternoon, Sade is sitting with Papa in his study. The study is a place of refuge for Sade from the intense heat. For Papa, it is a sanctuary where he can do some work whenever he's at home. It's because of Papa and Sade's similar behavior that Mama Buki jokes about their being like two beans from the same pod. They may not necessarily look the same, but they certainly act the same.