The only time I wear boots or "waterproof" shoes is in the snow. I do feel that they help when the temps. are cooler and snow is on the ground.
For 3-season use, the more breatheable the better. Your feet will get wet no matter what on an extended trip. The key is to learn how to deal with wet feet while hiking. I choose shoes that are comfortable and fast drying. I've tried "waterproof" versions of different shoes and my feet get wet from the inside out because of sweat. When these shoes do get wet, they take FOREVER to dry. I get highly breathable trail runners and will never go back.