(Minor correction: just like it has been in BotW, Blood Moons in TotK respawn only enemies and weapons/bows/shields in the overworld. Other actors, like regular animals, mushrooms, fruit on trees etc. respawn by a different gameplay mechanic based on RNG and real time)

....that being said, I totally get what you mean. I love playing these games as immersive as possible even to the point of making sure Link gets regular sleep and a hot meal each day regardless of whether or not he's missing health, and being careful with natural resources is part of that. I do mine every ore deposit I come across, but I don't take wild bird eggs out of nests (I buy them in Hateno instead) and often leave rare critters alone unless I need them for armor upgrades. Especially the fish on these Islands trigger this response, as they're rare, in a tiny and likely very fragile ecosystem, and might be the only food source for the "Sky Seagulls", so just taking them all away would mess up the food chain up there pretty badly. The same goes for apples - I have zero problems taking a lot of the apples in Hateno Village or other places where there are already plenty, but usually only take 1-2 from the apple trees on the sky islands. Everything else just feels wrong somehow.