The datacard applies to file extensions beneath where it is saved in the folder structure. I don't think you will be able to selectively apply it to different folders in the vault easily.
One alternative way you could set it up is so that tabs on the datacard will only show for particular users or groups.
Create your datacard with multiple tabs, one for each department. Then this one datacard can be saved at the top level folder and control the information shown on each file underneath based on what each department wants to see.
Check out this help file link to see how to do it: