Rinse the dried navy beans under cold water and remove any debris. In a large pot, combine the beans and water. Bring to a boil over high heat, then reduce the heat to low and simmer for 30 minutes. Remove from heat and let the beans soak for 1 hour. Drain and set aside.

In a slow cooker, combine the soaked beans, diced onion, molasses, brown sugar, Dijon mustard, salt, black pepper, smoked paprika, cayenne pepper (if using), chopped bacon, and apple cider vinegar. Stir well to combine all ingredients.

Cover the slow cooker and cook on low for 6 to 8 hours, or until the beans are tender and the sauce is thickened. Stir occasionally if possible.

Once cooked, taste and adjust seasoning if necessary. Serve warm.