I have no idea what percentage of Android APK libraries out there are using native code, but as Google has been pushing Intel tablets plus better compilers, every Android dev should certainly be aware of what's going on here. I figure that the only places where there will be real problems are when an app is carrying along some huge library (game engine, etc.) written in C or C++. That's obviously a problem for games, but it's less clear whether the problem goes far beyond.

As to Dalvik -> ART, I believe the picture is more complicated than it's been painted here. Dalvik was originally interpreted and then a JIT was added (in Android 2.2, says Wikipedia). ART has two separate backends -- a JIT and a "real" compiler based on LLVM. I have no idea how they decide which one to use at what time.

The idea of install-time compilation is old. Very old. Like IBM did it with System/38 in 1979 (later superseded by the AS/400 line). By distributing code as "vertical microcode", and compiling it when installed, IBM had the design freedom to completely swap out the underlying machine architecture. I believe the latest AS/400-compatible boxes are just PowerPC on the inside. It's smart for Android to follow the same path, since it means that whenever a new hardware features is available, the compiler can take advantage of it immediately.

So, yes, reinstalling Android is that much slower because you're recompiling all your apps. However, it's just not something that happens all that frequently. Besides...