The x86 customer base is such small, that i would not bother with x86 compilation at least not for Android. It just increases the verification effort.
It will run on the few x86 devices anyway, albeit quite a bit slower as you pointed out.
Thanks to Intel's contra revenue program 46 million tablets sold last year have Atom processors, and most of them (AFAIK > 80%) run Android. I'll let you decide if you still think that's a very small customer base. We had an issue with the app not working on x86 Android devices with Lollipop and the volume of mail we got about it did not feel small.
Were are talking strictly NDK here. So it is games mostly.
NDK is very commonly used in the most popular Android apps.
It's not just games. Maintaining your app completely in Java means you either have to have a completely separate codebase for iOS (and various other platforms) or you have to forget about them. It's much easier to just use something you can mostly run on all of them like C++ and therefore rely on the NDK.
If you are CPU limited it is the difference of 30fps to 10fps, which is big. In many cases however (causual games) you are not CPU limited at all. In this case you just pay the power penalty.
Well yeah. You can also go ahead and use a Saltwell over a Baytrail if this is what you run and you don't care. Of course, you don't just mean "not CPU limited" (using < 100% CPU time) here but using < 33% of CPU time, which is quite a gap.