I have a project organized as follow:
project/jni/Android.mk project/jni/libA/Android.mk project/jni/libB/Android.mk project/lib/armeabi/libA.so project/lib/arme
You can have the following in higher-level Android.mk files to recursively go through the directories. You'd put it in project/jni/Android.mk and it'd go into libA and libB and process the Android.mk files in them.
include $(call all-subdir-makefiles)