Google’s own services generate goo.gl short URLs (Google Maps generates https://maps.app.goo.gl/ URLs for sharing links to map locations), so I assume this shutdown only affects user-generated short URLs. Google’s original announcement doesn’t say as such, but it is carefully worded to specify that short URLs of the “https://goo.gl/* format” will be shut down.

Google’s probably trying to stop goo.gl URLs from being used for phishing, but doesn’t want to admit that publicly.