Mix the cocoa with the hot water and dark chocolate. Let it cool.
Place the flour, baking powder, salt, sugar, and baking soda into a large bowl. Mix gently.
Separately whisk the oil with the eggs, yogurt, and vanilla. Add the chilled chocolate cream. Homogenize.
Pour the liquid ingredients over the dry ingredients and whisk gently with a whisk or spatula until smooth. Do not overmix.
Preheat the oven to medium heat (180° C/356° F). Either line a 12-cup muffin pan with parchment paper or butter and flour them.
Pour 1 tablespoon of the mixture into each cup. Place 3-4 cherries on top. On top of the cherries, add more cupcake mixture so that the cups are filled almost to the top.
Bake the cupcakes for 20-25 minutes, until they pass the toothpick test. When ready, place them on a rack to cool.