Yes, native methods can be hooked. However, in case this is for an app's code, it has to be done after System.loadLibrary(), otherwise the latter overwrites the hook. Ideally, the framework should take care of this itself, but it's not straight-forward and the has been vey little need for this.
Tired of updating your mod for every new ROM release?
You want give users the possibility to combine different mods without creating tons of different files for all possible combinations?
Then have a look at my Xposed framework
- modifications without APK changes!