Yes many games have a galaxy map that shows where every thing is. The idea is the game randomly places the planets on a galaxy map (around suns and such). The amount of stars could be huge and you could see an area of how well you can scan (a large circle ect...).

Plus it means you can find a planet and add labels like I want to invade, drop from scan list ect...

This would add another view with some handy extra functions.

I really dislike this. Part of the flavor of game is the way you find planets randomly. Putting it on a map would ruin it.

I imagine a system of "jump nodes." Depending on how you scan and what your engines are like you have access to different sets of nodes and thus different planets.

It would have been nice if the designers had built the game around stellar systems instead of planets, but that's not going to change.

I'd say Wormholes rather than Jump Drives. There are several missions that involve Wormholes, plus there are Wormhole artifacts too. It would be more consistent.

Though It would be cool to have this, the only way im seeing this happening is if its done by sectors instead of planets. Planets already have greek and latin(I think) prefixes that make up half of their names. The prefixes could be used to organize planets by sectors, by naming the sectors after the prefixes.
As for planets without prefixes (dyson spheres, exotics) they could exist in the "Unknown" AKA the area between sectors.
Now the planets wouldn't get individual dots but if you click on the sector you would see a list of the planets youv found in those sectors.

Now if it were to be done this way, one could start giving planets of certain sectors certain qualities unique to that sector. And one could put NPCs of set rank variations in certain sectors. (AKA one sector has rank 1-10 NPCs, another has rank 20-30)

even though it is a "space" game the concept of actual space would be awkward to implement. Not just with the naming of planets but also the fact that it would mean nothing without some rather serious updates. Whoever made Masters of Orion would sue dan as well.

The biggest issue I see with this is this:
Planets in Galaxy: 397,198

the game is done well as is.

you are asking for 400 thousand planets to be organized and slapped into a system that doesn't exist.

Whats that Famous Maintenence quote from years ago? If it Ain't Broke, don't fix it?