According to my playthrough, and not taking new game plus in consideration (I may udpate about it later).
Husks and Husks groups : FINITE
Husks and husks groups never respaw, The body might still be visible, but you will never be able to interact with again.
I was never under the impression that husks location were random.
You will get the reputation bonus even if you don't know about the colony.
Ether Channels : FINITE
Ether : INFINTE
Unlike what is stated in the question, I didn't noticed one ether channel respawning in 120+ hours. There might be exceptions with high concentration ether places (like the castle entrance).
On other hand, at one point in game, it's possible to buy ether refils, ensuring you can't 'softlock' on ether (not that you will ever need it if you refrain for using ether channels once you max out).
Container : FINITE
Once opened a container will never close (and refil) again.
Skirmishes : INFINTE
Skirmishes reward : FINITE
Skirmishes respawn on reload like all monsters. unfortunatly, after the first try, you can't get new rewards, you can't even get the opposite reward.
Colony reputation : INFINTE
The three main way to get reputation are finite (husks, quests and skirmishes reward), fortunatly, there is a fourth way that is infinite if you come short: Encyclopedia cards. While the first time give you special reward, you can use them as many time as you can if you need to grind reputation.
Silver Nopon Coin : INFINTE
Gold Nopon Coin: Jury's still out.
During 95% of my game, I was under the impression that Silver Nopon Coin were a finite ressource. But in my post-endgame I started noticing auto-selling Silver Coins when fighting again unique enemies. It's clearly less frequent than on the first defeat, but it happens.
I didn't noticed it happening with gold piece yet, but I have hope with the 100+ level boss.
Note that the nopon coin are the 'pay2win diamonds' of the game. You won't need even one to complete the game. Their only usage is to skip grinding.
High level gems : INFINITE
Like Silver nopon coins, I started to worry about it until post-endgame, but I started noticing gems going in auto-sell when fighting again unique enemies. Like silver coin, the drop rate is way lower than on first defeat.
Airdrops : Jury's out
I'm under the impression that airdrop are completly randoms and infinte. But I'm not certain about it.
Spoiler fragments : FINITE
They never respawn, and you can only get one on the first killing of an unique enemies. I don't think there is a risk of auto-sell, and I never tried to sell them manually. I had 'enough' and spare, but for one shape, It was quite close.