For example, in AFPD, if I choose to increase the wingspan of a 60" plane to 120":
-- Does the plane look (cosmetically) any different?
You can't change the size of the plane with the internal program editor, you can only manipulate the plane that you have. BUT there is an external progam you can use to make the planes larger or smaller. See pic of the 2 OMP Edge Hybrids, they were created large, but these used an external application to be made small and then added E-power. If you change the dihedral or the angle of incidence of the control surface it will show your changes on the plane. There are hundreds of changes you can make.

-- Does the wing loading decrease automatically as a result or do I have to manually calculate how the wing loading would change and enter a value in a field?
What ever changes you make to the plane the software will detect it, you don't have to do any calculations.