The Bulbins and Bokoblins seemed to have a degree of sapience, with their camp organization and complex use of weapons, but they truly were monsters – possessed of evil magic and only vicious intent. What was more was that, whenever Link dispatched one and left the area, inevitably, it would be back when he’d returned to that area. There were several that he’d come to recognize – the one with the scar on his arm, the one with the runny eye, the one with chinks in his chain mail… When he’d killed them, he was never entirely sure that he really had, in fact, killed them. Clearly, there was something supernatural going on with them, and with most monsters. In their case, it wasn’t a moral dilemma – it was just frustrating. __ A Night on the Mesa, a Twilight Princess Fan Fiction by Shadsie.
Just one of my fanfics that dealt with this subject. Then again, in other fanfics of mine, I've just left carcasses laying there.... one of my AoL fics opens with Link yanking his bloody sword out of the body of a Daira.
I always figured that the blowing up and puffs of smoke and such were representational. They represented defeat - death in some cases, maybe not in others. In OoX, you're clearly killing evil beasts because you can get the Slayer's Ring. When it comes to human and more human-like oppopents, I am just not sure.
I can't see A Link to the Past's Link as being entirely heroic or the "good boy" he's supposed to be if he's actually killing those poor posessed guards. (You do have to to keep from dying), but I always figured that their "poofingn out" was representational of defeat rather than death (that the guards were exhausted and/or injured laying in the grass or zapped to the Evil Jar for a while to borrow a bit from the much-loathed cartoon). After all, they do return to the same spot if you go a few screens away and then go back and they look like exactly the same guys.
So, I guess I always imagined that the monsters faced bloody death but humans/innocents caught up in mind control and whatnot just got their rears handed to them.
At least that's how I write it all?