I don't get why this mechanic exists. Is it a trap to trick people into giving hunters kill targets? Every mil I seem to make harvesting is offset by 2-3 mil spent healing and rebuilding my troops after they are killed at a node. Are we really supposed to sit and babysit harvests for hours? Why is this designed this way? What am I missing?

You are not missing anything, you are just extremely unlucky when players are attacking your resource tiles.