Preheat oven to 350 degrees F (175 degrees C). Line 24 muffin cups with paper liners.
In a large bowl, mix together flour, 2 cups sugar, cocoa, 1 teaspoon salt and baking soda. Stir in oil, water, vinegar and vanilla until blended. Pour mixture into prepared muffin cups, filling each 2/3 full.
To make the filling: In a medium bowl, beat together the cream cheese, egg, 1/2 cup sugar and 1/4 teaspoon salt until light and fluffy. Stir in chocolate chips. Drop a heaping teaspoonful of the cream cheese mixture into each cupcake. Bake in the preheated oven for 25 minutes. Allow to cool.