Google Keep has a great solution for this. It just separates tasks that are still opened and those that are checked. I think it'd be a great feature to have in evernote. There is also a button to clear checked items once they are checked if you are no longer interested in seeing them.
I think the best way to manage check boxes is to have 3 options and the ability to implement different options for different notes.
1. When a box is checked do nothing just show the check mark.
2. When a box is checked move it to a "completed" section of the note.
3. When a box is checked archive the line item.