Rinse the small red beans, then place them in a pot with the water.
Bring to a boil over high heat, then reduce to a gentle simmer, partially cover, and cook until the beans are very tender, 1.5–2 hours; add a splash of hot water if needed to keep them submerged.
Drain the beans, reserving about 1 cup of the cooking liquid.
Heat 2 tablespoons vegetable oil in a skillet over medium heat, add the finely chopped onion, and cook until translucent and sweet, 4–6 minutes.
Add the cooked beans to the skillet and mash with a spoon or masher, stirring in just enough reserved cooking liquid to make a thick paste; season with the kosher salt and cook, stirring, until glossy and spreadable, 6–8 minutes.
Pour 2 cups vegetable oil into a wide skillet to a depth of about 0.5 inch and heat to 350°F over medium heat.
Fry the corn tortillas one at a time, pressing gently with tongs to keep them flat, until crisp and lightly golden, 45–60 seconds per side; drain on a rack or paper towels.
Assemble: Spread about 2 tablespoons hot refried beans over each fried tortilla.
Sprinkle each with the finely grated queso seco.
Drizzle with crema and serve immediately while the tortillas are still crisp.