Asserts should only interrupt your program while you are in the debugger. While this can be annoying while debugging, it doesn’t impact your shipping code, unless the assert results in a subsequent crash. One of the great things about JUCE is that you have the source code, so if this is too disruptive during development, you can just go in and comment out the assert while you are in development.
The problem here is that the jassert happens in the Juce String code, and commenting out the jassert from that is potentially a quite disruptive change as so many things in Juce use the String class. Detecting the corrupt/incompatible metadata should IMHO already happen in the Wav file parser itself.