Place the clams and 1 cup of water in a large pot. Cover and place over a high heat and cook the clams for 6 to 7 minutes. Uncover and remove the open clams.Cover the pot again and continue cooking the clams that haven't opened yet. Cook the clams for another 2 to 3 minutes. Turn off the heat and discard any clams that have not opened. Strain the liquid from the pot through a mesh strainer lined with a coffee filter and reserve.
Coarsely chop the clams and reserve.
Drizzle a few drops of olive oil into the bottom of the clam pot and toss in the bacon. Bring the pan to a medium heat. When the bacon has let off a lot of fat and become brown and crispy, toss in the onions and season lightly with salt. Cook the onions until they are very soft and aromatic but have no color, 7 to 8 minutes. Add the potatoes and cook for another 5 minutes.
Sprinkle the flour over the onions and potato mixture and stir to combine. Gradually whisk in the reserved clam juice. When the clam juice has been whisked in and there are no lumps, whisk in the milk and heavy cream and toss in the bay leaves and thyme. Taste for seasoning and adjust if needed. Bring to a boil and reduce to a simmer and simmer until the potatoes are cooked through, 10 to 15 minutes.
Toss in the reserved clams. Taste and re-season if needed and add hot sauce if using.