The way I thought of jump nodes and sharing tunnels is that each ship traverses their own independent tunnel depending on what frequency they used to open it. If everyone just picks the first random one that worked, then they'd all use different tunnels but end up at the same place at the same time once they exit.
If you can track a ship through subspace, it means you can know of its resonance frequency/pattern. Duplicate it, and you're in the same tunnel.
As for cargo, I figured that somehow the docking mechanism does something to carry the object through subspace with it. I guess if the coupling mechanism was too complicated, it'd be impossible to get a human pilot, and all the secondary ordinance, to follow his/her ship into the rift. Maybe simple contact is in fact all it takes.
I do agree though, using subspace as a weapon would probably introduce all sorts of weirdness. Because it messes with space time and contact with parallel universes, people probably don't want to abuse it that much.
@ Luis: yeah, whoops >.>