You mapped for q3. So you know there are textures and shaders. In the textures menu you can see the folder names which are inside the base/textures folder (yes, in the assets0.pke also have a textures folder) and the shader files' names too.
You don't rip the textures from actual maps. They are grouped by map name mostly but not always. You will see that this is very comfortable when you want to use custom textures.
It is possible that in a shader file there are shader definitions but for textures in an other dir. There is for example the imperial.shader file which contains lots of shaders but for other sets. That's why sometimes you don't get any textures when you select a set.
GtkRadiant uses the radiant/notex texture if you don't select anything. That is in the mapextras.pk3 or mapextras2.pk3.
Hope I could help.