Resources are probably only transferred when planetary ones are exceeded.
That is my understanding, it allows you to make use of linked planets resources, since the "trade" of goods between linked planets is instantaneous. In other words large planets with lots of links make very good fleet building planets. Its not a part of the game I really like, but that might be because I have no links. The chance of a link increases as star density decreases, so I assume it is to counter the disadvantage you encounter with a empire in an area of scattered stars.
