The scorpion is the chosen symbol or crest that El Patrón uses for his family. Having a family seal is a sort of old school practice. Think medieval knights or feudal landlords. Often, even today, wealthy, powerful families have a crest that has symbolic meaning for their house or family. So in The House of the Scorpion, the word house refers to the Alacrán family, and the scorpion refers to the symbol that El Patrón has chosen to represent that family.
Phew. We've got that part down. But why the scorpion in the first place? They're not exactly friendly creatures. Plus they're really ugly (sorry, scorpions, but you know it's true). They're poisonous, sometimes lethal. They're sneaky, and hide from view until they sting you. Starting to sound familiar? El Patrón, too, is sneaky and dangerous, and he's definitely lethal. Plus, it doesn't hurt that scorpions are known to be desert creatures, and Opium is a desert country. So maybe El Patrón has picked a creature that he thinks is a fitting representation of himself – a powerful, terrible desert-dweller.