Most modern smartphones run Android, which means they have a bastardized Java VM between your "native code" and actual metal... not unlike having a JS VM.
It's not that "native software" has become less efficient, but rather that it is slowly disappearing.
As of Android 5.0, the Android Runtime (ART) compiles Dex bytecode ahead of time to native code. That probably still isn't as efficient as C++ or the like, because there's still a garbage collector, and Java methods are virtual by default.
It's not that "native software" has become less efficient, but rather that it is slowly disappearing.