The primary API was provided in Java, so yes from the NDK for many needs you have to step back to Java-world momentarily. This is a simply a limit of time however (given that Dalvik was their primary app runtime for other reasons) -- Google has been pushing more and more functionality directly to the NDK (e.g. 2.2 gives you the ability to fully use OpenGL from native code).

However that is neither here nor there. You have the full ability to fall to native, to go hog wild with memory references and uninitialized pointers and stack overflows and trying to break free of the box you are placed within (the process boundaries). You have the ability to include C code from other projects for codecs and processing, etc.