I agree about this being an issue. Evernote "fixing" something that does not need fixing. The Checkbox is relegated to a drop down whilst the Checklist is promoted to prominence. I use the Checkbox, for example when shopping - it serves as a visual reminder of needed items that will be needed again. I don't need/want strikeouts.
The WORST of it is that is you hit the enter key in the middle of a Checkbox list, ALL the list immediately converts to a Checklist. And there is no undo option. That shjould be optional and it appears that EN wants to think for us again...