A shudder in the loins engenders there (line 9)
To "engender" means to create or bring to life: Zeus impregnates Leda. The "shudder in the loins" clearly refers to the completion of the sexual act. It's not certain whose loins are "shuddering." When it comes to body parts in this poem, Yeats frequently leaves out the possessive pronouns like "his" or "hers."
Before the indifferent beak could let her drop? (line 14)
Zeus adopts the animal nature of the swan and acts "indifferent" toward Leda once he has gotten what he wanted. He has no human emotions to express to her and doesn't care about what happens to her. He has been holding her by the back of the neck, and now he releases her to the ground.