I just wanted to add that I too am experiencing this issue with MacOS. I have notes that are tagged but are not showing up when I click on those tags in the app. However, on the web version and iOS version the notes do appear. I've signed out and signed back in multiple times, shut down, restarted my computer, removed the tag and added it back, but yet nothing seems to fix this.
My entire evernote system is Tag based so this is quite an issue and I would prefer not to have to use the web version.