I think the number of planets in a system (and annexed planetoids, satellites, dwarf planets, asteroid belts, and other celestial bodies) should be handled by the game settings (density and types). Naturally this would also affect the human solar system (the real one), as long as it still is somehow close to the real thing because it would look weird if we played human with Earth and Jupiter only (according to the settings).
I agree the best solution for satellites (m00ns) is to have them attached and orbiting to their planet.
Just like the m00n orbits around Earth right now, so it should be for all the other m00ns (we're talking of Jupiter and Saturn right now but it should work the same for all planets and m00ns, again, according to the density settings).
I also agree that the thing be managed at planetary system level. Which means the m00ns are considered to be part of the planet and the playercolonizing a planet has colonized the whole system (m00ns included and here we could use some technology to drag the m00n's resources with more efficiency to the planetary structures).
The fact here is that we've got a 2d game based on strategy more than arcades (I take SOTS2 as reference). It is turn-based, and if you are one level below the competition you must at least add a level of depth.
To me a level of depth is making space somehow realistic. I think you're figuring it to be harder than it really is.
The game is turn-based so it's all about dciding the TIME unit and then, according to this TIME unit, decide how many units are needed for a planet to be in one hex or in the next one (following its unseen orbit around its star). Faster (closer) planets move more hexes but if you target a planet with movement or action the ship would still get there in that turn because the system takes that motion into account when calculating movement range.
Question: How long in TIME is a turn? How far can a ship travel in the timing interval? That is how you end up calculating how many hexes a planet can travel in that time interval, according to its orbit. And it doesn't necessarily need to be a WIDE movement (obviously ships move faster than planets, a lot faster!)
The m00n is orbiting around a planet that is not moving. The sun is spinning on itself and it's not moving. The comets and asteroid belts are not moving or rotating... the galaxy image beneath the hex layer is not moving.
But AFTER the turn processing is complete you will see space is dynamic because a planet could have changed hex, that comet will have moved, the galaxy background beneath the hex layer will have changed by a very very tiny bit (which implies the spyral is rotating).
This is very important... it's not a cheap suggestion with no consequences.
It will spell whether or not this game is complete fantasy or it has at least some accuracy. The Universe should be dynamic, it's not a painted crap onto a hex layer.
There are TACTICAL and TECHNOLOGICAL aspects that will be unlocked if this is developed in this way and we're obviously neglecting a huge opportunity in depth if we keep it 2d and totally static.
EDIT: Read carefully: the first thing is to assess the time scale, then the movement scale which should include a dynamic universe.