There are different folders for different architecture, There is a high possibility that you have not provided your Native Libraries for a specific architecture that you are currently debugging on.
Kindly copy your .so Libs in these folders aswell.
I hope this helps.
Edit:
Please add the feature as required from the list below in your Manifest.xml
file :
<-- require OpenGL ES version 1.0 (default) -->
<uses-feature android:glEsVersion="0x00010000"/>
<-- require OpenGL ES version 1.1 -->
<uses-feature android:glEsVersion="0x00010001"/>
<-- require OpenGL ES version 2.0 -->
<uses-feature android:glEsVersion="0x00020000"/>
<-- require OpenGL ES version 3.0 -->
<uses-feature android:glEsVersion="0x00030000"/>
Dynamic Liner Library :
Please go through This link : NDK OpenGL undefined reference to glVertexPointer