I have completed said mission tonight, but I didn't understand a number of things.

1) I boarded the ship, unlocked the cargo but somehow didn't get it. How could I have actually gotten the cargo? It's also a bit illogical that I don't get paid for it anyway since Fish says they are going to recover the ship.
2) I flew back to the place mentioned in the mission description and that meant the guy could just run off. This was not at all clear. I guess I could have gone to the place the guy mentioned but it's just really badly indicated what the consequence of going to which station is.
3) There is no time indicator even though there is a 48 hour limit and no proper resolution, you have to remember to mail fish after 2) is done and wait for his answer.

I'm sorry, while the mission is good the resolution is pretty confusing.

If you really want to you can watch my journey here and see my confusion: https://www.twitch.tv/videos/395065146?t=01h28m25s

I don't know if I agree to your critisism, I thought the mission was pretty clearly explained. I'll try and help. In one of his beacons John says

"Around 2 hours ago something collided with us [...] The impact tore off a large section of out aft quarters.... The hold, stores and the workshop breached [...]"

The hold was blown off in the impact, there is no cargo to retrive. Mr. Fish gives you a bit extra for compensation but not the full amount since the cargo is gone. In the dialogue John says:

"[...]where will you take me? If you take me back to Adari, they'll probably kill me you know.[...]"

To which you can reply:

"I'm not sure you deserve to die for this. Maybe I'll take you somewhere else instead."

This is summaried by john as:

"I have no choice. My life is in your hands, captain. You decide where to take me. I'll get off the second I'm able, no matter what. If it's Adari, I'll face the consequences. If it's not, then I guess I thank you... for understanding."

So at least it was clear to me that if you leave him to Adari he will face a trial, and if you leave him anywhere else you're letting him go, forgiving him for his crimes. I agree that there should be a mission timer on the quest missions. I'd like to be able to read mail and navigate on the same time, or pause while you are reading your mail and news. Especially on this mission there is a lot of reading and it's dangerous to not watch the nav computer and you're on a time limit so you don't really want to stop.

Thanks. It wasn't quite clear to me that the equipment I had to retrieve was lost in the incident. On the St Stella Maris there is also this button to let go of the cargo, so it looked very much like it was there.
The extra compensation was because the trip was longer and more involved than initially anticipated. Yes, I saw Adari in the Dialog, yet the mission description mentioned another station. On top of this there was no reason for me to go to Adari in the first place. I wouldn't go to Adari except to deliver him, so it makes little sense for him to jabber on about not wanting to go to Adari. Yes, it's indeed a lot to read and a dangerous area. I suppose there is a clock somewhere, but a lot of missions have a dedicated timer, just not this one. It causes a severe feeling of uncertainty.

In my case it was even more dangerous because I ran into a asteroid belt on purpose. There was a beacon in the asteroid belt and I thought I had to go very close to it to get the message. My ship was nearly destroyed before I gave up. The distance at which beacons sync seems to be pretty random. I don't know whether I got anything off this particular beacon, I think not. So I had to navigate most of those dangerous systems with a heavily damaged ship and pay 1100 credits for the repairs, making the entire two hour mission almost a loss.