I'd like to setup different domains like department1.domain.com, department2.domain.com, ecc. The store can share customers data, currency, billing settings etc, but should have different root categories. So, I think I can use one website and different stores, but I'm not sure about the URL configuration because it is at Store View level. In this case, have I to use different websites to configure different third level domains? thanks
For the base url it would not really matter but I'd go with different websites since it gives you more flexibility. There are more options in settings on website level than store level.
In general I would only use stores for either a different language (so just translations) or minor differences in design but nothing more