In cases where an applications desktop file has more than one category, it appears in each of the matching submenus. Like thunar, orage, terminal ... As the spec states *Note that at least one Main Category must be included in the desktop entry's list of categories. If multiple Main Categories are included in a single desktop entry file, the entry may appear more than once in the menu.* This is obviously conform with the spec, although the *may appear* leaves it to the implementation, how to handle that. If it shouldn't be handle withing garcon, these apps should probably be *fixed* or tweaked in distributions.
As you pointed out correctly, apps may appear more than once and I think this is fine. We have no one-appearance-only policy and even if we did, I'm not sure how we would go about choosing one of the categories in a smart, automatic way without knowing anything about the app in question.