Why did the Messenger of Allah, peace and blessings be upon him, brand the eyes of those who killed the shepherd and drove away the camels, even though that is not mentioned in the verse of Hirabah?

The hadith you asked about is that narrated by Al-Bukhari and Muslim from Anas ibn Malik, may Allah be pleased with him. The story of the 'Urayniyyin is that they came to Medina and fell ill. The Prophet, peace and blessings be upon him, ordered them to drink from the urine and milk of camels. When they recovered, they killed the Prophet’s shepherd and stole the camels. So, the Prophet, peace and blessings be upon him, ordered their hands and feet to be cut off, their eyes to be branded with heated nails, and them to be thrown in the Harra.

The Prophet, peace and blessings be upon him, branded their eyes as qisas (retribution) because they had done the same to the shepherds, as Muslim narrated from Anas: "The Prophet, peace and blessings be upon him, branded the eyes of those people only because they had branded the eyes of the shepherds."

Scholars have unanimously agreed that what the Prophet, peace and blessings be upon him, did was a lawful qisas, not a forbidden mutilation; because they had gouged out the eyes of the shepherds and cut off their hands and feet, so they were recompensed with the like of their deed. Sheikh Al-Shinqiti said: "He branded their eyes only as qisas because they had branded the eyes of the shepherds of the pregnant camels." Ibn Al-Qayyim said: "The offender is treated as he treated others, for when they gouged out the eye of the shepherd, he gouged out their eyes." Ibn Hajar said: "It is a similitude in qisas, and that is not part of the forbidden mutilation."