Hi Enric,
The MoGraph options are Beat-, Camera-, Color- and Multi-Shader. I assume that you have the shader[s] in mind that work with an ID or the clone color itself.
There is no native solution for this “work” to my knowledge. I guess it needs to be done with an individually created Python script, to produce all the Texture Tags (or the export data thereof) first, then apply the textures, if the Multi-Shader is in question, etc.
The only way I could see is camera mapping, but I have my doubt that this will work, as each clone needs to be visible to the camera.
My suggestion, as a developer of plug ins, or the Maxon Support, if they have an idea:
http://www.maxon.net/support/support-questions.html
Less likely that you have the time, but a suggestion would be cool:
http://www.maxon.net/support/suggestions.html
Good luck.