We have a Cordova app that begins on a local web page then immediately redirects to a remote page, and we have recently had a bunch of users on iOS 9.3 complain that they are just stuck on the first screen.

So it looks like it probably does affect Cordova apps.

This could potentially be an issue with any app that uses an association file.

edit To clarify, you need to use an association file on your website that references your app. What triggers the bug seems to be unknown, but appears to involve shared credentials.