Not as far as I am aware, and I am not seeing anything other than managing teams. Ultimately this is something Evernote who would determine if this was supported not Jamf.
For you to be able to manage an application with a configuration profile, the developer of the application must support managed preferences. Then they must have a keypair that controls the setting you want to configure. Evernotes identifier is com.evernote.evernote, and this is what a configuration profile would target. However, it does not look like Evernote supports managed preferences, assuming you could sort out what the keypair was.
I will give one last bit of caution. I would not want to disable auto updates on any application, especially not one that handles possibly confidential data. By not keeping Evernote up to date, you are hampering any reliability in the data being transferred is secure.
In the end, this is something I would suggest reaching out to Evernote over.
