Separate clam meat from the juice setting the juice aside.
If necessary chop the clams to small 1/4" pieces and reserve.
Drizzle a few drops of olive oil into the bottom of the 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.
After 5 minutes toss in the reserved clams and simmer for an additional 5 to 10 minutes until the potatoes are cooked through.
Taste and re-season if needed and add hot sauce if using.