In a large paella pan or wide, shallow skillet, heat 1/3 cup extra-virgin olive oil over medium heat. Add 1 large onion, finely chopped, and cook, stirring occasionally, until translucent, about 8–10 minutes.
Add 2 cloves garlic, minced, and cook, stirring constantly, for 1 minute, until fragrant.
Add 14 ounces cleaned squid (bodies and tentacles), cut into rings or bite-size pieces. Increase heat to medium-high and cook, stirring occasionally, until the squid is opaque and has released its liquid, about 5–7 minutes.
Add 1 large ripe tomato, grated, and cook until the mixture has reduced and thickened, about 5 minutes.
Stir 1 1/2 teaspoons squid ink into about 2 tablespoons of the hot fish stock until dissolved, then pour the ink mixture into the pan and stir until the sauce turns deep black.
Add 1 3/4 cups bomba rice or other short-grain rice. Stir for 2 minutes to evenly coat the rice.
Pour in 4 cups hot fish stock, season with salt to taste, and scatter 7 ounces peeled shrimp evenly over the top. Bring to a boil over high heat and cook for 5 minutes without stirring. Reduce heat to medium-low, cover, and simmer for 13–15 minutes, until the rice is tender and most of the liquid is absorbed.
Remove from heat, cover with a clean kitchen towel or aluminum foil, and let rest for 5 minutes. Serve with aioli on the side.