In a medium saucepan, bring 3 cups water to a boil. Add salt, then spaghetti, and cook until al dente, about 7-8 minutes. Drain, reserving a few tablespoons of pasta cooking water.
Meanwhile, in a small skillet, heat olive oil over medium-high until shimmering. Add garlic and cook until just golden brown, about 2 minutes. Immediately remove to a paper towel to cool. Reserve the oil.
In a medium mixing bowl, whisk together miso paste, and 1 tablespoon pasta cooking water until smooth. Add cooked spaghetti and toss until evenly coated, adding more pasta cooking water if needed for consistency. Add lemon zest, red pepper flakes, and scallions and toss.
Transfer to a bowl, drizzle garlic cooking oil over the top, grate over some parmesan cheese, and serve, adding extra pepper flakes if you wish.