I've taken to just closing Evernote completely when I'm not using it ... and favoring other tools I have when Evernote is not the obvious best choice.
This approach makes the tool less useful, but also far less annoying.
There's a management concept that's been around for decades -- "Management by exception". The idea is that reporting should highlight things out of the ordinary; you do not bother people with information that's by definition non-actionable. (It's why 'error messages' are frequently used, but 'health messages' less so.) Evernote designers appear to be unfamiliar with