Obviously I only use disable for apps that I can't uninstall. Having said that, I've never experienced a disabled app updating. For me when disabling an app I usually clear the cache, data and uninstall the updates before disabling it. It might be worth it to enable the app just so you can take those steps. Although I'm a little surprised that you can't uninstall Evernote altogether, but if you can't and haven't taken the afore mentioned steps try them and see if they work for you.
Meanwhile, I'm new to the Samsung universe so it may work differently on their devices, but is the app from the Galaxy Store or the Play Store? For me with the latter if I see the app, in a list or "My Apps" on the Play Store, it just shows as being installed but is also labeled as disabled and I've never seen a disabled app show up in my update list. As for the former, I sometimes get notifications that apps have updates but I only select apps that I use or want to update. I'm not sure how many Samsung apps I have disabled on this device but for the most part I just ignore the ones I don't want and manually update the ones I do or don't mind having at least.