I'm not sure why wad.js would specifically be different as it looks like they are using the Web Audio API similar to Hype. Maybe you have unchecked "Use low latency Web Audio API" in your Hype document? (Hype may sometimes automatically disable this as well if it can't quite figure out if the environment supports it, like if you're loading from a file URL)
Other than this, my shot in the dark would be wondering if you've added the UIBackgroundModes Info.plist key with an array with an audio string entry?
I did some internet sleuthing and it sounds like there was a similar bug in iOS 13 but that one at least got fixed a while ago.