I would write a script that does it. Essentially what you are trying to accomplish a sense of realism which would require a set of rules similar to the planet generation tech aKA "Stellar Forge". POIs get randomly generated based on your set of rules on planets. Things that the rules would consider are whether or not the planet is in the human inhabited space, the amount of traffic, system status, how far the planet is from the bubble, whether the planet is located in a known alien area, whether the planet has lots of mining potential (generate mining outposts), whether the planet is located in lawless system (generate planet pirate base) etc.... There are many rules that can be taken into account.
the script would place Points of Interest in non atmospheric planets (for now) like crashed exploration probes, crashed ships, basically all the POIs they currently have in the game now that you can find. It would place these POIs on planets across the galaxy as persistent locations. These POIs could be countless and the diversity would be up to the developers. They can add new ones as they create new content.
Once a month or whatever timing the developers decide based on their rules, they can clear these out and then run the script again to generate new POIs for the galaxy. Some of these POIs like a crashed exploration probe could trigger a mission for you to return the data to a station back in the bubble somewhere for a huge reward and reputation bonus.
Note: These POIS would not affect the hand placed POIs like Barnacles and Alien Ruins that are specifically placed in certain places. And this hear shows you they have the technology to generate persistent POIs already. What they need is a script with a set of rules that generates the other countless planets with POIs and the ability to refresh or to update these at a given time like I say once a month or every other month. That is what I would do at least.
You could also do a very similar thing with USS. Instead of generating them around the player, generate them through a script that gets run once or every other month.
I forgot to say that the player needs to have tools to find all these things. A deep surface scanner should reveal the location of anomalies on a planet surface to make it easier to find things. Not every planet has to have POIs.
The player also needs tools to find USS that are persistent. A scan of the system should reveal anomalies in space and a deep surface scan of a planet should reveal anomalies located on the planet.
After thinking about this a while, I have a few problems with it.
Many/most/(all?) POI and USS contain resources, ships, or datapoints. If they are persistent, you'll eventually drain a system of these resources, and have to wait until the month or so until it all resets. And there will be no more distress signals for a month? For many of the USS and POI's, as they are, the current setup is kinda more realistic after the fact (though there are exceptions).
USS:
***Distress signals\weapons fire detected are definitely temporary, so would make more sense to pop up around the players. (be cool if they had a time limit and eventually change to combat aftermaths.)
***Destroyed ships in space (CA, DE, EE, HGE) can be seen as pretty temporary. Often a rescue ship is already there when you show up. If you don't pick up canisters or what not, one of the NPCs will, as well as the scrap metal, or anything that will give off a signal source. I'd also like to occasionally see large junker ships arriving to collect the debris while you're there. That'd add realism to why it's temporary. Now that I think about it, modules that allow you to collect scrap and recycle them to reusable metal to sell would be awesome.
***Convoy dispersal patterns are stupid and shouldn't exist... Why aren't these ships in supercruise???
The point is that there are tons of NPCs, and they'll eventually clean up stuff.
Planet POI:
*** Any debris guarded by skimmers is going to get cleaned up as soon as whoever owns them shows ups and gathers the goods/scrap.
*** Debris not guarded by skimmers probably will be soon.
Planet POI buildings:
Buildings and such are the exceptions, though abandoned stuff would probably be salvaged by NPCs eventually.
For things like buildings on planets, I think the discovery should still be random around the player, but the location gets saved to a save file on your system, and it becomes semi-permanent. Then if you want to show someone else your find, you can synchronize this save with friends. Though depending on what it is, it can also be temporary, just with a longer life. Same with things outside the bubble.
The reason I prefer this to your idea is that you're not ally discovering the things your way. You're honking and then going to the question mark. I like the idea of "stumbling upon" something. Just coming across it, rather than activating a scanner then going to the question mark. Sure it's an illusion, and the universe is manifesting something near me, but from the character's perspective, it's functionally the same. On the other hand, if it was all persistent, the odds of just stumbling upon something are so incredibly high, you instead have to be told almost exactly where to look upon entering the system. And since you're being shown this as soon as you're enter a system, you either have A) everybody being shown the same few things in each system for a whole month. B) Only show a small selection of possible things each scan. (But then what decides what gets chosen?) C) Litter every system with thousands of POI every scan.
The way it is now, there's a chance to find stuff just about anywhere.