It doesn't. But there could be some issues if you try to enter Canada and you are asked questions about employment status which is rare. Usually an officer just checks work permit validity dates and that's all.
You don't need to show the back of the photo for online applications.
1. It may, but very unlikely.
2. Yes, you'd better.
3. It won't replace, the officer will be able to see what you have sent via the webform.