Preheat a grill to high. Place the whole eggplants directly on the hot grates and close the lid. Turn occasionally until all sides are charred and the eggplants are very soft and collapsing, about 20–25 minutes. Remove and let cool in a bowl.
Make the spiced breadcrumbs: heat a large sauté pan over medium. Add 1½ tablespoons olive oil, then the breadcrumbs. Stir and sprinkle in the cumin, chili flakes, salt, and pepper. Toast, stirring, until the crumbs darken slightly and dry out, about 5 minutes. Remove from heat and stir in the chopped dill. Transfer to a plate and wipe out the pan.
Prepare the eggplant-walnut sauce: cut cooled eggplants in half and scoop out the flesh (you should have about 2 cups). Drain any excess liquid, then add the flesh to a blender with the soaked walnuts, lemon juice, miso, about ½ teaspoon of the minced garlic, and salt and pepper. Blend on high until completely smooth and creamy.
Cook the pasta in a large pot of boiling salted water according to package directions. Reserve 1 cup of the pasta cooking water before draining.
Return the sauté pan to medium heat and add the remaining 1½ tablespoons olive oil. Add the diced shallots and the remaining minced garlic and cook, stirring occasionally, until the shallots are soft and translucent, about 5 minutes. Reduce heat to medium-low.
Add the blended eggplant-walnut sauce to the pan, then add the drained pasta and a big pinch of salt and pepper. Stir to combine, thinning the sauce with reserved pasta water as needed to reach a creamy consistency.
Serve the pasta hot topped with the spiced breadcrumbs and extra chopped dill; add extra chili flakes if desired.