I think you do not understand that the disappearance of the thumbs has nothing to do with the crucifixion. It is a common way to represent hands folded in the Middle Ages. Here’s an example. Bonifacio Bembo (1420-1482), Court of the Sforza family, Bergamo, (http://www.myartprints.com/a/bembo-bonifacio/people-of-the-court-of-th.html ).
Maybe the lack of thumbs is more common then we think. But then again, it being common in how folded hands and arms are depicted doesn’t really mean that it “has nothing to do with crucifixion” also. It being common doesn’t mean the shroud is art or a photograph or fake in any way. But it does change the argument that the lack of thumbs is somehow convincing.