Melt butter and honey in a small saucepan over medium heat or in a microwave-safe bowl. Pulse graham crackers in a food processor until fine crumbs form. With the motor running, drizzle in butter-honey mixture and process until well combined. Transfer mixture to a medium bowl; set aside.
Using an electric mixer on high speed, beat cream cheese in a large bowl until creamy, about 3 minutes. Add condensed milk and beat until smooth. Add key lime juice and lemon juice and beat to combine. Beat in 2 Tbsp. key lime zest.
Using a whisk or electric mixer on medium-high speed, whip cream in another medium bowl to very soft peaks. Sprinkle powdered sugar over cream and continue to whip until it holds stiff peaks. Gently fold 1/2 cup cream into key lime mixture; cover remaining cream and chill.
Line muffin pan with paper liners. Pour key lime mixture into a pastry bag or plastic bag with the corner snipped off and pipe batter evenly into tins. Top each with 1 1/2 Tbsp. cracker crumb mixture, breaking up crumbs to completely cover, then press down gently to adhere. Freeze until set, at least 3 hours.
Remove pies from molds, turn upside down, and remove paper liners. Spread reserved cream over pies and top with remaining 1 Tbsp. key lime zest.
Pies (without topping) can be made 2 weeks ahead; cover and freeze.
