I used the missions a lot in GC3, but I have only sent out 3 or 4 missions in over 500 hours of play in GC4SN.

I found attaining and keeping #1 status in miliary rank stops a lot of AI aggression towards my civ, but keeps my yards busy building ships. 

If someone has tips on how to use missions effectively in the current form please let me know. 

Maybe scavenger missions to boost elerium, etc so you can retrofit existing ships with the newest technology from time to time.

I didn't know that treasure hunting missions can get that low. Those missions got changed so they have a bigger range of high and low results. You just happened to have got a really low result.