Weights: These are only affecting the AI planning routes and they are covered somewhere in the Documentations folder of the modtools. They will not affect the height of the hubs. I suggest not to experiment too much with them until you understand how they work.
Changing the altitude of your Hub:
First, place your hub. Then you raise the terrain and the hub will follow upwards. *EDIT* - I just saw that you already knew about this, however I know of no other way, alas.
Another altitude issue are the spawnpaths, and they are much simpler:
Changing altitude of a SpawnPath Node:
Hold "shift" when moving it with your mouse.