Preheat the oven to 350 degrees F (175 degrees C). Line 24 muffin cups with paper liners.

Whisk flour, 2 cups sugar, cocoa, baking soda, and 1 teaspoon salt together in a large bowl. Stir in water, oil, vinegar, and vanilla until combined. Spoon batter into the prepared muffin cups, filling each 2/3 full.

Beat cream cheese, remaining 1/2 cup sugar, egg, and remaining 1/4 teaspoon salt in a medium bowl until light and fluffy. Stir in chocolate chips until incorporated; drop a heaping teaspoonful into each cupcake.

Bake in the preheated oven until cupcake centers bounce back when gently pressed, about 25 minutes. Allow to cool before serving.