In a medium bowl, whisk together 1/3 cup oil, the lime zest and juice, chopped mint, thyme, chile flakes, garlic, salt, and pepper. Pour half into a small bowl and set aside.
Add shrimp to remaining marinade mixture in medium bowl and chill, covered, about 1 hour.
Meanwhile, cut peel from watermelon, then cut fruit into chunks about 3/4 in. by 1 in. Heat a grill to very high (550° to 650°).
Thread watermelon onto six to nine skewers (8 to 12 in. long) so pieces lie flat. Brush on both sides with remaining 1 1/2 tbsp. oil. Thread shrimp onto six to nine more skewers, piercing each through its top and bottom to form a C (so shrimp lies flat).
Grill watermelon on one side only until grill marks appear, 1 minute. Transfer to a platter. Grill shrimp, turning once, just until pink, 1 1/2 to 2 minutes total; set on platter.
Drizzle skewers with reserved marinade and sprinkle with torn mint.