Hallo Corybe,
you are totally right. If you connect your Evernote account to any third-party tool, you will grant access to your notes. As developers could change the code in any way, every developer could change code so that note content could be accessible to him/her. Even Evernote themself could theoretical access your notes. Nevertheless, we respect your privacy and it is totally not in our sense to access your notes without your approval, otherwise we would risk our complete business model.
At Filterize, there are exactly two persons at the moment, that have access to the production code base, which includes access to the database keeping your Evernote access token. That's me and one of our developers. Both of us have no interest in your notes. Also there are laws, that we have to keep your privacy, especially here in Germany.
Concluding we can say that, yes you are right, there is a potential risk, but we're doing everything to keep your privacy. If you want to be totally safe you have to keep your notes locally on your machine.
Best regards,
Pascal