I am having a similar issue. The YouTube vids work in my mobile ready version and not when the file is converted to an .apk format.
To give you a little more context, I packaged the app using Adobe Captivate. I embedded web objects that pull the https:// files from youtube (all youtube vids now have the https:// start). I ran a debugger on the app and it says it can't find the youtube video/that there is a youtube video error. Instead of pulling the youtube file with the https:// beginning it is converting it into file:// at the beginning. I had a developer look at it and he says that it may have to do with permissions.
I'm not a coder and I have looked at the documentation for integrating YouTube into an app, but I'm not clear where to put that code since I've published using Adobe Captivate. Also, we tried to set some permissions in the XML file that I had to create and those aren't seeming to work either. Do you have any resources/support contact that I can reach out to in order to get this problem resolved? If not, is there a way to package my already mobile ready version of the site into a hybrid app? Thanks.