I have noticed that toktx tool doesn’t have an option which allow to create 3d/array texture. Why ? Do you know some other way/tool which allow to create ktx array/3d texture ?

Because I did not have the time or inclination to do it before. But I have just finished adding this along with mipmap generation as part of the KTX Version 2 work.

You can also use GUI tools such as PVRTexTool and Compressonator to create such textures.