Just on OP's point about 'invisible' ships, it happened to me at the weekend. I was doing a run from Robi with about 8 missions stacked, had completed either three or four and was undocking from a station.
*Please read this before you waste your time telling me about authority patrols and how to smuggle*
This isn't my first rodeo. I know the authority patrol the entrance to stations. I can see them on my scanner. I always line up with the slot inside the station, wait until the gap in the patrol appears and then leave at full boost with 4 pips to engines, boosting repeatedly until I'm clear to jump. This is in an Asp which at the time the incident at the weekend happened was boosting at around 380, slightly down from its maximum of 395 due to the cargo I was carrying. I have never and I do mean never been scanned on leaving a station. In that ship, at that speed. I've been scanned leaving an outpost once when there was an authority ship lurking outside which scanned me before I could get off the pad, but never leaving a station.
More to the point there were no contacts on my scanner at all when it happened and critically there were no contacts in my contacts list either. I was about 6k out from the station and just to head off the last suggestion, no it wasn't a commander running silent because I was in solo.
I assumed it was a glitch and the game had basically spawned a ship which for some reason I couldn't see.
The fact that I've only even thought to mention it in response to the kicking some people are giving this guy should tell you how much of a life-changing experince it was for me, I thought 'meh' and headed off to do something else, that was the sum total of my reaction so I'm not raging about it at all. Stuff happens.
All I'm saying is that yes, we've all see the posts from noobs who don't have a clue about how the smuggling missions work and I know it's easy to dismiss any comment about stuff like this because of them but what OP describes is exactly what happened to me. This weekend was the only time it has ever happened to me in coming up on 5 months of playing the game (I don't mean failing Robi missions, I mean being scanned without being able to see the ship that is doing it, anywhere at all, whilst doing anything, ever) and it was out of the ordinary enough for me to comment to a mate in chat when it happened.
I've done runs from Robi with 14 missions stacked in the past and haven't experienced the issue so it's clearly a one-off and I doubt it's specific to smuggling, I think it's more likely that we hear about those incidents because a Robi run is the only time it will cause you to lose a few million in potential income.
Regardless, it definitely happened.