Why did the Horyuji temple in Japan have a second story?

Answer: To emphasize the structures significance

They were able to be built because of the support of a man called Prince Shotoku, who was considered to be a great statesman and a founder of Buddhism in Japan. The story of how Horyuji Temple came to be is engraved on the back of the halo of the Yakushi Nyorai Buddha statue, which is in the temple's main hall.