The only thing I can imagine is that most of the joystick floating around weren't wired for it, and so game developers didn't want to rely on it.
Or something.
I don't know why, the amiga is perfectly capable of accepting a 2 or 3 button input.
I do remember an Amiga Power article where the writer was lamenting game controls, and wondering why nobody ever used the keyboard. Maybe it was too "IBM"