Pick over beans; rinse well.
Place in a large bowl with cold water to cover by 2 inches.
Let soak for at least 6 hours or overnight. (Or use the quick-soak method: Cover the beans with 2 inches of water and bring to a boil; simmer 2 minutes. Remove from the heat and let stand, covered, for 1 hour.)
Drain.

Heat oil in a soup pot or Dutch oven over medium-high heat.
Add all but 1/3 cup of the onions, bell pepper, celery, jalapeño and garlic and cook, stirring frequently, until the vegetables are beginning to brown, 5 to 8 minutes.
Add cumin and cook, stirring, 1 minute more.
Add the beans, water, coffee, ham hock (if using) and bay leaf;
cover and bring to a boil, stirring occasionally.
Skim off any foam that rises to the top, reduce the heat, cover and simmer until the beans are very tender, 1 1/4 to 1 1/2 hours.

If using, remove the ham hock and set it aside to cool;
remove the bay leaf.
Stir in salt
Puree about half of the soup in a blender or food processor until fairly smooth. (Use caution when pureeing hot liquids.)
Return the pureed soup to the pot and heat through.
If desired, cut meat off the ham hock, trim away any fat and chop the meat into small pieces; stir back into the soup.