Beat the cream cheese on medium-high speed in the bowl of an electric mixer until fluffy.
Blend in the sugar until smooth. Mix in the salt and ube extract.
Beat in the eggs one at a time, mixing well after each addition.
To assemble, spoon 3 tablespoons of the cheesecake batter over the crust in each cupcake liner.
Bake until the filling is set, about 22 minutes.
Remove from oven and top each cupcake with a sprinkle of latik.
Transfer to a wire cooling rack and let cool to room temperature.
Transfer to the refrigerator and let chill for at least 4 hours before serving.