In a large Dutch oven over medium, combine the oil and pumpkin seeds. Cook, stirring often, until fragrant and lightly toasted, about 5 minutes. Using a slotted spoon, transfer to a small bowl; set aside.
To the pot over medium, add the onion and 1 teaspoon salt. Cook, stirring occasionally, until softened but not browned, 5 to 8 minutes. Add the flour and cook, stirring constantly, until evenly moistened, about 1 minute. Add the zucchini and dill stems, stirring well, then stir in the broth and 2/3 cup of the toasted pumpkin seeds. Bring to a boil over medium-high, then reduce to medium and cook, uncovered and stirring, at a vigorous simmer, until the zucchini is translucent, 5 to 10 minutes.
Remove the pot from the heat and cool for 5 minutes. Using a blender and working in batches so the jar is never more than half full, puree until smooth; transfer each batch to a large bowl.
Wipe out the pot, then pour in the puree. Cook over low, stirring often, until heated through, about 5 minutes. Off heat, stir in the dill leaves and lemon zest, then taste and season with salt and pepper. Ladle the soup into bowls, dollop with crème fraîche (if using) and sprinkle with the remaining 1/3 cup pumpkin seeds. Serve with lemon wedges.