I am not sure it makes a difference, as cities and depots (and forts and harbors etc...) are all 'structures' in essence.
Nevertheless, since BOA, we used to have cities and harbors located in the cities tab, while forts and depots are located in the setup tab... reason at the time (and still now) was that cities are supposed not to change much in name and size in the course of the related conflict, while forts and depots may change a lot (in terms of ownership, destruction, etc...)...
Pocus may complete my answer if I forgot something...