Hidayat, the Athens gold medal winner playing his fourth games, offered no respite for Koukal, who claimed the 40th and last berth in the draw after New Zealand and the Netherlands withdrew their nominees.
"I prepare the same, no matter what rank they are," Hidayat said.
He should wrap up his group on Tuesday when he faces Pablo Abian of Spain, thereby setting up a likely last-16 playoff showdown with defending champion Lin Dan of China.
Koukal, after carrying the Czech flag in the opening ceremony, was happy just to be at his second Olympics, even on the wrong end of a hiding. He was diagnosed with testicular cancer in late 2010, and though it was in remission he was still recovering.
"About a year ago I was not sure I would be alive," he said. "It's winning just being here."
Other winners included European champion Marc Zwiebler of Germany, Son Wan-ho of South Korea, Jan O Jorgensen of Denmark, and Kevin Cordon of Guatemala, last year's surprise world championships quarterfinalist in the same Wembley Arena.
In women's action, gold medal tip Li Xuerui of China thrashed Claudia Rivero Modenesi of Peru 21-5, 21-6 in 22 minutes. Li only made the draw this month, after a 30-match winning streak lifted her into the top-3 world rankings.
No. 6-seeded Juliane Schenk of Germany, Bae Yeon-ju of South Korea, Anastasia Prokopenko of Russia, Susan Egelstaff of Britain, Anu Nieminen of Finland and Neslihan Yigit of Turkey also won their group openers.
Grace Gao of Calgary and Vancouver's Tobias Ng lost 2-0 to Denmark's Joachim Fischer and Christinna Pedersen in their opening mixed doubles match. In women's doubles, Wang Xiaoli and Yu Yang of China beat Toronto's Alex Bruce and Michele Li 2-0.