To be clear, not all employees of the company can see your notes. Only Evernote employees that need access for the specified reasons will be able to, and they'll be "subject to background checks and receive specific security and privacy training at least annually to ensure they are up to date on the latest privacy and security requirements and standards." The firm says that the list is kept "as small as possible."
If you're an Evernote user, you do have some options. For one thing, you can opt out via account settings, under the section "Allow Evernote to use my data to improve my experience". The company says that if you do this, you won't be able to get the most out of your experience, although it would probably be more surprising if it didn't say that.
The other thing that you can do is encrypt your notes. You can do this from the Windows or Mac clients, and the company says that once you do, no one will be able to access your notes without the password.
Finally, you can do what many seem to be deciding on, which is to use another service, such as Microsoft's OneNote. You'll have until January 23 to make up your mind, as that's when the new policy goes into effect.
Update: Evernote has since changed course, saying that this will now be opt-in, rather than opt-out.