Preheat the oven to 350 F. Arrange the phyllo shells on a baking sheet and bake for 4 to 5 minutes, until crisp and lightly golden.
Cool the phyllo shells completely so the filling will remain thick and the shells will stay crisp.
Blend the cottage cheese, Greek yogurt, vanilla protein powder, powdered sugar, vanilla, orange zest, and cinnamon for 1 to 2 minutes, until silky.
Fold half of the mini chocolate chips into the cottage cheese filling. Refrigerate the filling for 30 minutes to firm it slightly.
Spoon the chilled cannoli filling generously into the cooled phyllo shells shortly before serving.
Finish the cannoli cups with the remaining chocolate chips, chopped pistachios, and a light dusting of powdered sugar.