Take a much closer look at the mission description. First, the part that says "Hostile ships may be sent against you." And second, the mission ranking. It may not be a trading rank, you may get what seems like a nice, simple pickup or transport mission, that recommends an Elite rank in combat... that will tell you something about what you'll be up against.Yeah I definitely tried scooping and jumping out but I was shot down too fast every time. Really sucks but I guess I just have to deal with it if a similar thing happens on future missions. Is there anything I can outfit my ship with at all to better my defenses (either by weapons or otherwise) or do I basically have to wait until I get a better ship to even attempt to deal with NPCs?
Now, in terms of salvage missions specifically, don't be under the impression that you have to pick up every single piece of salvage before you leave. There will be more than one USS spawn for salvage. Pick up one or two if you can and GTFO before the bad guys show up and get a bead on you. Then just fly around until another Mission USS appears. Rinse, repeat.