For the fried shallots: Heat 1/2 inch oil in a small skillet over medium; attach a deep-fat thermometer to skillet. When oil shimmers and reaches 320 degrees, carefully add half of shallots. Cook, stirring occasionally with a fork, until shallots are just golden and bubbles stop forming rapidly around them, 2 to 3 minutes. (They will darken and crisp as they cool; do not let darken in oil, or they will taste bitter.) Transfer to paper towels, season with salt, and let stand until cool and crisp. Repeat with remaining shallots.
For the tuna: Pat fish dry. In a small bowl, combine 1 teaspoon flower of salt, 1/2 teaspoon pepper, and sesame seeds. Sprinkle mixture evenly over fish, patting with fingers to adhere; let stand 5 minutes.
Heat a heavy-bottomed skillet (preferably cast iron) over medium-high until very hot and wisps of smoke are visible, 2 to 3 minutes. Add tuna and cook, undisturbed, until bottom is golden brown and releases easily from skillet and fish is opaque about 1/4 inch up sides, about 1 minute. Flip fish and cook on second side about 1 minute more. Transfer to a cutting board; let stand a few minutes.
Meanwhile, whisk together soy sauce, vinegar, oil, and ginger for vinaigrette. Slice fish into scant 1/4-inch-thick pieces. Arrange on a platter for sharing or on 4 individual salad plates. To serve, drizzle vinaigrette evenly over fish and sprinkle with shiso, shallots, bonito, and flaky sea salt.