In a 3- to 4-quart pan over medium heat, stir cherries, 1/2 cup granulated sugar, orange juice, lemon juice, and vanilla bean until cherries are juicy and sugar is dissolved, 3 minutes. Adjust heat to maintain a simmer; stir occasionally until cherries are soft, about 10 minutes. Remove from heat; if making up to 2 days ahead, cover and chill (reheat before serving).
Meanwhile, in a bowl with a mixer on low speed, beat mascarpone, cream, vanilla, and 2 tablespoons granulated sugar until soft peaks form. Cover and chill up to 2 days (if needed, whisk to thicken before serving).
In another bowl, mix 1/4 cup granulated sugar and the flour, cocoa, baking powder, and salt. In a bowl, beat egg to blend with milk and butter. Stir into flour mixture until evenly moistened.
Turn a waffle iron to high heat; spray both sides lightly with cooking oil spray. When hot, add about 1 1/4 cups batter; close iron and cook until waffle is well browned, about 9 minutes. Remove waffle; keep warm on a baking sheet in a 200° oven up to 15 minutes. Repeat to cook remaining waffles.
Place a waffle on each of 6 dessert plates; sprinkle with powdered sugar. Top with cherries and juice (discard vanilla bean), then mascarpone cream.