Native phone application performance or C++ performance
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"Native code" means native to the processor. The processor does not understand Java or Swift. Swift is also compiled into "native code" whereas Java is usually compiled to bytecode which is then converted to native code by the Java VM. So, at least in theory your C++ Qt app should be faster than Java on Android and has the potential to be as fast as Swift on iOS (if not even faster according to a recent study). QML, however, is a different story: By default this is compiled at runtime (though there is an option to pre-compile it, I think). You might still include some code in JavaScript with QML. JavaScript generally performs worse than Java.
Generally speaking, you don't pay a performance penalty for using C++ on these platform. But, you might pay a performance penalty for using QML because it is not using native GUI elements (as far as my knowledge goes; I don't use QML personally). For most apps I doubt you'll notice the overhead of using QML.
Maybe someone with more experience using QML can chime in.