Microsoft Windows is built around hooks. Most of them are hidden behind their api but once your application becomes anything more then trivial you can't get around using hooks once in a while.
It's not a matter of ethics, it's just how windows is built.
To put it even stronger: a windows program that uses the windows ui can't work without using hooks.
The act of using hooks to interface with other programs can't be considered evil or not evil. It's what you do with your program that makes it evil or not.