Preheat oven to 350 degrees. Place paper liners in two 12-cup muffin pans and spray lightly with cooking spray.
In a medium bowl, mix together flour, cocoa, and salt. Set aside.
Measure buttermilk in a glass measuring bowl and add baking soda and vinegar. Stir to combine. Set aside.
In a large mixing bowl, use an electric mixer to beat the shortening on medium speed until light and fluffy.
Slowly add sugar while continuing to beat at medium speed. Stop once or twice to scrape down sides of the bowl.
Add eggs one at a time, scraping down sides of bowl between additions.
Add food coloring and vanilla.
Reduce speed to low and add the dry ingredients, alternating with the buttermilk mixture, beginning and ending with dry ingredients.
Fill muffin cups 2/3 full. Bake for 20 to 25 minutes. Cool completely.
For Icing, place cream cheese and butter in a large mixing bowl and beat until light and fluffy using a hand mixer or stand mixer. With mixer on low speed, gradually add sugar and vanilla and beat until smooth. Frosting will be fairly thick.
Spread on top of cupcakes with a spatula or use a pastry bag for a more decorative look. Decorate with sprinkles.