The app uses the extension, and the app is really only a shortcut to the extension. The apps page is just a collection of shortcuts, may be to extension, websites. There may even be a way to add shortcuts to local programs and files, though I haven't tried. Nevertheless, if the app depends on an extension, as Hangouts, Docs, and Sheets do, then removing the extension will also remove the app. Removing the app also removes the extension.
As an extra note, websites added to the desktop by Chrome, which also show up in the apps, can be removed from either place without affecting the other. I have removed the desktop shortcut to Super User, but kept the app shortcut.
Why Google offers Hangouts in either format, when they end up being the same is a mystery known only to them. The other Google items I've used, limited as that is, are only offered as one or the other, even though they end up in both anyway.
There may be apps for Chrome that, after installation, only use local resource or independent access to Internet resources with no need of Chrome's extension system. Such may install only to the apps and not the extensions. I haven't used apps enough to verify that.