I would expect it indeed to have either been scooped or shot by an NPC.
The shepherds make inviting targets, as do the cargo flocks that they are shepherding. So much so that it does actually point this out in the readme.
Can a Cargo Shepherd get sucked into a wormhole? On a recent trip I was carrying 2 of these useful devices, and deployed them both during a fierce firefight between traders, pirates and me. Wormholes then appeared to open near both Shepherds, but I had no time to investigate as I was busy mopping up the few remaining pirates. When the battle was over, one of my Shepherds had vanished. I didn't know if it was scooped up by some lightfingered lowlife, shot, collided with at speed, or somehow disappeared into the wormhole.
(I should explain I have little knowledge of wormholes and how they behave as I haven't yet investigated that aspect of the game).
Thanks for such a wonderful expansion. I have recently started doing a lot of mining and thought it would be wonderful if the Cargo Shepard would pull in splinters as well as cargo pods. I saw a comment about that earlier in this thread, but wondered what you thought of the idea. From a code perspective I believe it should be fairly simple.
It is fairly easy to do - I think a way to do it was posted in the OXP tweaking thread in this forum section.
I've retired from making and supporting OXPs, but many of my OXPs have been adopted by others and they are supporting them. Unfortunately this one is currently orphaned and not supported by anyway, but if someone wishes to do so and make such a change then they are welcome to do so.
.