Can't reproduce the problem, maybe something wrong in the DS settings?

-Did you have cargo ships enabled before installing EEM?
If not: try removing EEM, enable Cargo ships/drones and encounters and Check if they despawn as well.

-Do you use Server extender or something else to clean your map automatically?
Try changing Server clean up Settings

What visibility distance do you have in world's settings?

We have set it to 7km for performance increases on planets and yes we had cargo ships enabled and they do spawn sometimes. We did not change the settings from default when we created it which had everything enabled.

And our server is just a privat hosted one without any extensions or something.

So the issue occurs because of visibility range too low, the game just keep spawning them outside that 7km... For now - increase it to 10 or 15 km, but you had a point - I guess we should modify our cleaning script - instead of just "remove grid when beyond visible distance" add condition "if range below 12 km - remove on 12 km distance", so it will be possible to play with those visible settings :)

We will try that then, would love to see that update comming so we can go to planets without having to play on 15fps :D

And 7 km distance helps with that?

For us it does, exept when we are in space then its a lot better

It never helped me on planet's surface, no matter what distance was set, the fps was the same :(