@baco we are battling these issues heavily right now. A prototype which we built long ago, but just recently decided to release, was working fine over past two years, but as soon as we dove into to re-factoring it to utilise WKWebView, we have no end of issues, including now not being able to open external URLs.
Unfortunately, the app runs fine in the Monaca IDE preview, as well as in the debugger, and in a custom debugger we built.
We can get links to open in a clean app built from scratch - so we suspect there must be some cached components or code that are interfering with the build. 2 weeks into troubleshooting, and we are no further than when we started towards fixing it.
Our app works fine, but will no ability to open a system web browser (which should be the simplest thing ever in the whole world. :)
Will be adding a new issue referencing WKWebView - keep an eye open for it.