A re-analysis of Yehohanan in 1985 revealed that his forearm bones did not show nail damage, and the nail in his heel was too short to go through two heel bones. It also theorized that his arms were tied to the cross, while his heels were nailed separately on the sides of the cross.
Since there seems to be no standard procedure in crucifixion, it is highly possible that crucifixions involved both nails and rope, depending on the materials available and the cruelty of the executioners.
It is long thought that the nails were placed on the hands and feet of the crucified. But archaeological evidence say otherwise, as with the case of Yehohanan’s remains.
Much of the doubt on nailing hands and feet stems from suspicions that these appendages may not be able to support the weight of a crucified human body.
Furthermore, it is thought that latter translations of the Gospel may have mistranslated the Greek word for “wrists” or “limbs” into “hands.” The Gospels were written and initially translated into Greek, the lingua franca of the Middle East at the time.
Therefore, when the resurrected Jesus was said to have displayed his wounds to his disciples, he might have been showing his forearms instead of his hands.
In any case, as crucifixions seemed to follow no standard procedure, extra nails might have been placed on hands or feet or on any other extremities of the body for the sake of cruelty rather than practicality.
Various methods of crucifixion meant various causes of death on the cross.
A popular theory states that exhaustion asphyxia was the main cause of death. Hanging on the cross caused the arms of the crucified to stretch tight, overstretching chest muscles and making breathing difficult. Victims struggled to rest stretched limbs until they were exhausted and died slowly of asphyxiation.
However, due to pre-execution tortures and other cruelties on the cross, victims could have died of other causes like hypovolemic shock (catastrophic blood/fluid loss), cardiac arrest, and infection.
If victims were healthy upon crucifixion, starvation, dehydration, exposure to the elements and hypothermia could have killed them.
Death might come in hours or within several agonizing days. Executioners, however, could choose to hasten death by stabbing the victims or breaking their legs.
Publicly displayed, the crucified would have been a horrifying sight – with victims seen as either naked mutilated bodies, or living, delirious and squirming on the cross until they die.
Bodies were often left to rot on crosses to humiliate them in death and to serve as a public warning. Sometimes, however, the Romans permitted bodies to be taken down for burial, as what they did in the case of Jesus, whose remains were taken down and buried before sunset following Jewish custom.
After Christ: crucifixion elsewhere in the globe
Early Christians identified themselves with a fish symbol called "Ichthys" and rarely with a cross since it was an instrument of torture and execution that claimed the lives of many Christians. In the 4th century, the Romans legalized Christianity and made it their state religion. They abolished crucifixion out of respect for Jesus Christ. By the 5th to 6th centuries, the image of Jesus on the cross became a Christian symbol.
However, crucifixions and similar punishments were still carried out across the globe long after the Romans abandoned it.
During the Song Dynasty in China, state criminals were executed via “slow slicing” – they were nailed to a bench-like frame and slowly cut into tiny pieces.
Feudal Japan practiced two forms of crucifixion: one where victims were tied to a cross and speared to death, and the other where victims were tied upside down to crosses planted on a shore and left to drown.
Medieval Islamic states used crucifixion to punish heinous crimes according to certain interpretations of Islamic law.
Saudi Arabia continues to punish heinous crimes with crucifixion, though those sentenced are beheaded first and the headless body tied to a metal frame for public display. – Rappler.com
Sources: Crucifixion in the Ancient World and the folly of the Message of the Cross by Martin Hengel, A Tomb in Jerusalem Reveals The History of Crucifixion and Roman Crucifixion Methods: Biblical Archaeology Society, Roman Crucifixion Methods Reveal the History of Crucifixion: Biblical Archaeology Society, Medical Aspects of the Crucifixion of Jesus Christ by David Terasaka, M.D. , The Wars of the Jews or the History of the Destruction of Jerusalem by Flavius Josephus, Medical Theories on the Cause of Death for Crucifixion, On the Physical Death of Jesus Christ by William D. Edwards, MD; Wesley J. Gabel, MDiv; Floyd E. Hosmer, MS, AMI, Dr. Craig Evans on Jewish Burial Customs, Gunnar Samuelson: Crucifixion in Antiquity, Diego R Yuki on the 26 Martyrs of Japan, Water Margin: Outlaws of the Marsh by Shi Naian, Amnesty International: Saudi Arabia: Five beheaded and 'crucified' amid 'disturbing' rise in executions, 21 May 2013.