How do you feel about the ethics of the master ball? What if that technology could be reproduced by criminals? Also, would they work on a pokemon that already belongs to someone? I’m scared for my little baby wailord. He’s fragile!

The master ball is just another poké ball, only with an increased capture rate. So if there was anything unethical about it, then there would be something unethical about poké balls in general, in my opinion. After all, you could catch a legendary pokémon with a poké ball just as you could with a master ball; it will simply take more of the former than the latter.

Ultimately, the tool isn’t the problem; it’s the intent. If you used a master ball on a pokémon because either they wanted you to catch them or because you fully intended on taking good care of them, that would be perfectly fine and ethical. However, if you were a criminal intending on using the master ball to poach pokémon or to use a pokémon for nefarious purposes, then that wouldn’t be right, but again, it’s not right because of what you intend to do, not how you go about achieving it. So yes, I would be bothered if Silph allowed the schematics of the master ball to fall into the hands of a criminal organization, but I highly doubt that would happen.

As for your final question, rest assured that poké balls in general—including the master ball—cannot work on pokémon that already have a trainer. This has to do with with the fact that a conflict of trainer’s IDs (that is, the act of attempting to apply a trainer’s ID to a pokémon that already has one without first deleting or editing the original through releasing or trading, respectively) actually decreases a ball’s effectiveness to a dramatic degree. This renders a normal poké ball completely ineffective (a pokémon will always break free, even if they’re not trying to do so) and a master ball practically so (a pokémon will break free if they will themselves to do so).