Drain the cottage cheese in a fine mesh strainer for 20 minutes. Preheat the oven to 375 degrees F and arrange the phyllo shells on a baking sheet.
Bake the empty phyllo shells for 4 to 5 minutes, until crisp and lightly golden. Let them cool while preparing the fillings.
Blend the drained cottage cheese, lemon juice, lemon zest, and salt in a food processor until smooth and fluffy. Refrigerate the mixture until needed.
Cut the halloumi into 24 small cubes. Heat the olive oil in a nonstick skillet over medium-high heat and cook the halloumi for 1 to 2 minutes per side, until golden.
Fill each phyllo shell with whipped cottage cheese and top it with a warm halloumi cube. Drizzle a small amount of hot honey over each cup.
Sprinkle the cups with pistachios, mint, and crushed red pepper. Serve immediately while the phyllo and halloumi are crisp.