Jesus came to earth to die for our sins. It doesn't matter which way. The Roman cross was a torturous way. He could have been beheaded, hung, shot through with arrows or speared. Does the details really matter. If a large nail was between fingers, His body weight could have torn the hand away between the fingers. Some therefore think He was nailed in the wrists. Does it really matter? Little details like this doesn't really matter for a Christian. Research on Roman crucifictions show sometimes peoples arms were tied to the crossbeam before nailing. Sometimes, if no one claimed the body, they were left on the cross to rot.
Jesus being a Jew, and by Jewish law, had to be brought down from the cross to be buried quickly. So, somehow they got the nails out. At that time, they made swords, hammers, saws, scissors, catapults, and other metal tools. So they probably made a crowbar, which would have been easier to make than a sword, saw, or scissors.