Artpunk
My opinion on this is that WKWebView was changed in iOS10 by Apple (loading of assets, audio system), and changes were made with C2's implementation of WKWebView to be compatible. This has adverse effects, particularly being broken on iOS8 (thank god so few ppl still use this) and has potential issues with iOS9.
What you should have tested though is the latest Cordova WKWebView plugin in XDK. See if that helps first since 1.0.3 is ancient and there have been lots of fixes since.
Also if you've minified during C2 export, don't do it.
I read that thread on TA, seems it's fixed with your recent update! Was it by using a more recent plugin?
ps. Just noticed it was 3 days ago, so that's pretty quick that Apple release updates. It used to take 10-14 days for updates to go past reviews, so launching a game with bugs on iOS = DEAD.