Hi Marta, I don't know enough about the use-case to be sure. However my suggestion would be to use the organisation units to represent the departments. It is simply because usually the departments are different across hospitals - some are not always there, some are combined and so on. So you could make a script that creates the initial setup with all departments in all places and then modify it from there. It makes form design easier. The data mart performance penalty mentioned above applied at the time of writing but not anymore with the analytics engine. A problem with using categories is that you get lots of non-applicable fields if you use section forms, and lots of maintenance mess if you go with custom forms.
cheers Lars
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