Is it possible to get the Zoltan Shield/Engi Med bot dispersal etc through random encounters?

Solution 1:

Neither one will show up in shops or as random rewards. However, there is one event that occurs at distress beacons in Engi sectors that has a guaranteed med-bot dispersal as a reward.

There's an Engi ship being attacked by rebels. After you defeat the rebel ship, you choose to give them some resources. Give them 40 scrap, two missiles, and two fuel, and they'll give you a med-bot augment.

As far as I know it's not possible to get the Zoltan shield or other "special" augments / subsystems outside of starting with them.

Solution 2:

Now, in AE, the Zoltan shield augment can be obtained from the Zoltan Cruiser quest, with 50% chance. The other possible outcome is maxed out Zoltan crewmember named "Envoy".