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Sharingan should be able to see through mokuton clones. Shadow Clones are different from Mokuton clones due to shadow clones being the actual real bodies duplicates of the user. Shadow clone consist of flesh and bone and the same chakra reserves of the user.
Mokuton clones are nothing more than vegetation that has less chakra than the original. The chakra signatures are different due to the clone having less chakra and different body composition from the user.
So Shisui's MS will see thru Mokuton Clones. If Hashirama had a shadow clone then it would be a different story.
Wrong. Out of the entire Uchiha clan Madara said his visual prowess was the only one able to see through them. Unless you're implying Shisui's Sharingan=Madara's Sharingan Shisui doesn't have such a feat.