this SOUNDS like a great, logical idea, but sometimes the boss isn't around, or is very busy and doesn't wish to be disturbed for something as mundane as instructions for sorting papers. Many bosses/managers/etc. delegate some of the daily runnings of the workplace to other employees, and expect that they'll distribute the work correctly. Obviously, we have no idea what kind of boss OP has, but if it was a situation like above, OP wouldn't think to ask the boss about something like that, because it wouldn't be common practice. I know I sure wouldn't ask my boss for clarification of something like that, even if she did happen to be in the office, because that is not the way things work.

I see your point, but the purpose of the email would not be to ask the boss anything, only cc:ing him/her so that there is a record of what the coworker told them to do. But suppose you're right and the boss didn't want to be bothered - then a simple email to the coworker before starting the sorting task would have saved their butt and avoided the their word against mine scenario.