("...having too many mines on an individual planet will make the game run more slowly when there are lots of enemy ships there...")
Addressed in 2.001X/Z, right?
Not really, that was about the slowdown that mines cause just by existing if there are huge numbers of them. If you stack too many mines all at one planet, and there are a ton of enemies, the slowdown caused by that is not particularly mitigated. However, in most cases the "slowdown" is such that it won't even affect the frame rate at all on a midrange computer (since except in the largest battles, on a midrange dual core computer the primary is probably 30% idle or even more -- so in this case, it would just be dipping into that 30%, which I prefer not to do so that there is more buffer remaining for the larger battles).
So it's not something that has been addressed directly, in summary, and it's something that makes me wary, but it's not much worry with the current numbers of mines. But if you stack all 3,000 mines on one planet, that might cause some noticeable lag if a lot of enemies come there at once.
Again, though, are ALL ships in the proximity affected by Area Mines/etc., the similar way Grenade Launchers work? I would imagine having 1 mine damage potentially a thousand ships when they emerge from a wormhole be cheap--though I will have to see inside the game for actual results.
Yes, all ships are affected by area of effect ships. I know you're concerned about this, but so far you're just giving theoretical arguments that it concerns you; in practice, I have never seen a problem with this yet because ships automatically spread out. Also, you may not be aware, but when ships are fading in from a wormhole, they are invulnerable to being shot at until they are fully faded in, which also means that they are then more dispersed -- thus greatly negating the effects you are worried about.
On the other hand, you just reminded me that I don't think that ships that are fading in are immune to area of effect explosions (even though they are to regular shots), so there is some possibility for undue casualties there. I'll take a look at that probably tomorrow night for that ZA release, and that should shore up any potential for wormhole-related abuse of AoE attacks.