I made an app for Android - ported an emulator written in C++. (Link in sig, if you're interested, but this isn't a slashvertisement.)
So the core of the app, the 'engine', is in C++ and must be natively compiled, while the UI and such is in Java. Naturally, the binary's compiled for ARM first. This actually runs on a lot of Intel Android tablets because they have ARM emulators. But, thanks to a user finally asking, I put in some time and now I can make an Intel version. (Heck, the original source was written for Intel anyway, so it wasn't a big stretch.) The existing tools are sufficient for my purposes. And it runs dramatically faster now on Intel.
However, for the developer it's mildly painful. The main issue is that you have a choice to make, with drawbacks no matter which way you go. You can include native libraries for multiple platforms, but that makes the APK larger - and according to a Google dev video I saw, users tend to uninstall larger apps first. In my case, it'd nearly double the size. So instead I'm putting together multiple APKs, so that ARM users get the ARM version and Intel users get the Intel version - but only Google Play supports that, not third-party app stores. I haven't looked into other app stores, and now it's less likely I will.
Note that native development can be important to apps for a non-technical reason: preventing piracy. An app written purely in Java is relatively easy to decompile and analyze, and pirates have a lot of techniques for removing or disabling licensing code. Adding a native component makes the app much harder to reverse-engineer, at least delaying the day that your app appears on pirate sites.