Now, someone correct me if I'm wrong.
When it comes to jumping from system to system, I pretty much assume that the target location within the destination system can be pretty much anywhere within the system (modulo 100D limit et al). I also assume that there is some margin of error (i.e. you don't pop in at some exact point in space, but reasonably close).
Next, I would think that since (as I understand it) your original Real Space vector is maintained through the jump, you would want to get a vector heading towards your destination planet (wherever it is plotted to be, probably completely unrelated to your current planet), or you simply stop the ship, jump, and create a new vector when you arrive.
My concern with regard to piracy, is simply that if you essentially allow ships to come in system with any vector, and allowed to arrive within any part of the system, that patrol of the system would be neigh impossible. The resources required in terms of just the volume of patrol vessels would be utter madness.
The reason is two fold. The first is simply gettting enough ships to effectively cover the vast area of space with sensors roaring to extend their reach, but more importantly, two, is to have patrol vessels close enough that their response time is meaningful. It simply does not matter how many patrol craft you have if they can not get to the ship in distress in any reasonable amount of time.
So, given those two details as a premise: ships can arrive pretty much anywhere within a system, regardless of their starting system and the wide open space is simply unmanageable from from an actual patrol point of view, doesn't it make sense that systems will have designated "injection" areas and trade lanes to the planet?
The idea being that if you limit where ships can come in to the system, and the routes they take once in system towards the planet, then you vastly reduce the number of patrol craft necessary to provide security to the shipping lanes, and still have effective coverage and response time.
Now certainly there is nothing to stop you from coming in to a system whereever and whenever, but the systems traffic authority can make compliance to their injump, outjump and trade lanes a condition on whether they will be able to provide security for your vessel.
Assuming the routes are efficient, there's no reason a trader wouldn't take these routes. Even though planets move et al, etc. there's no reason these publish routes can't be made relative to the host planet, and no reason any normal star chart wouldn't have that information. It's just another minor detail in your jump planning.
The only downside is for those ships that aren't willing to take the time/fuel to change their vectors from a fixed location for the destination planet.
Even if that were the prevailing view then the in system patrol can set up and patrol the common vectors for ship egress, from the common trade partners. Most planets have very few trading partners within J-1,2 or even 3, and that leaves a finite number of "optimal vectors" where folks should be coming in to the system, and where they should be exiting the system.
It would seem to me that without these kind of restrictions, piracy would be much easier to do, much like pickpocketing on the New York subway, just too much to police.
Especially if the pirate is operating near the 100D limit, it seems that the pirate can easily evade an approaching patrol by simply jumping outsystem. It doesn't even have to be a particularly GOOD or really accurate jump, just "close" to get the ship out of the system, even if it were a micro jump out into deep space. Burns a week, but better a week spent in J-Space than a life on a prison colony.
On an unrelated note, some folks questioned how to dispose of a ship once you've captured it. If you're talking about just getting rid of it, I think that would be fairly easy, shut it down so it's a cold rock, and just push it off the elliptic plane into deep space, or toss it into a nearby Gas Giant or star.