This is because pjsua-app is not generated by default on the general build (more specifically, pjsua:
target is not included on all:
target at pjsip-apps/build/Makefile). To fix this just go to pjsip-apps/build and run:
make pjsua
This would create proper object files at: pjsip-apps/build/output/pjsua-arm-unknown-linux-androideabi/ (needed when building android sample).
Once you've all corresponding object files, you can run ndk-build again at pjsip-apps/src/pjsua/android