Aside from black soul gems, it does not seem that too many ethical concerns have been raised regarding trapping of souls in the Elder Scrolls universe, on this matter, I can only assume one of two things is true. Either there ARE people who question the ethics of such a thing but they're simply not represented in the games, or no one cares since none of those entities whose souls are trapped are people. Perhaps no one objects to the practice for the same reason why you probably wouldn't feel bad about swatting a fly.
It also must be pointed out that, in Morrowind, enchanted items would recharge on their own, suggesting that the soul would permanently exist in them and continue producing power for the enchanted item. If you think about it, this may be an even more unpleasant fate.
That's true, especially with the Daedric weapons, which users can occasionally hear or experience cries and torment from. But well, it still does bother me considering it does seem that not all Daedra are evil in the mortal sense, they are simply chaotic and a lot are very much sentient.
Don't confuse game mechanics with lore. As far as the lore is concerned by capturing a soul you capture the identity of something. Think Redgaurd, Feyfolken, and probebly a few more.
Oblivion is the first game that completely treats the soul gems as batteries. In Morrowind you could capture unique souls and in Daggerfall what ever was trapped would come out occasionally when your weapon broke.
Do forgive me, but I do not really understand this part. Does this mean that individual souls are not captured? As in, if Fargoth the Bosmer was captured, it would be a Bosmer's generic identity that is captured, but not Fargoth's individual soul? Thanks again!