Using scent is actually a good idea. Even though zetsu is changing his body to mimic the persons chakra and appearance, you cant actually mimic thier DNA. Zetsu will still be zetsu regardless if he transforms his body and chakra into someone else, so he will still be giving off zetsu pheramones, which kiba can sniff out. Thats why they put him on guard duty.
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Another thing they can do to check people (at least to gain acess to the medical area) is have a member of the yamanaka clan check thier memories. If it shows them being stored in an underground cave, then its a zetsu. Its a little risky since you have to touch the person to read thier mind, but its an option