When used correctly, I think it can be very good. I use treats (not a clicker though, I usually just cluck) to train my horses to do tricks. It's a fun way to spend time with them and increase their trust in you without necessarily riding or working them.
However, I have seen MANY people use it incorrectly and they just create monsters. The horse needs to learn to be polite about taking the treats, and certainly needs to learn that they will NOT get treats by mugging you. Also, there are some horses that I just won't hand-feed treats. Last winter I worked with a little morgan with some serious respect issues. His owners gave him lots of treats...I did not. After months of working with him, I thought one day that he would be fine if I gave him a little treat...he reverted back to his old, pushy self. After that I would just put them in his bucket if I wanted to give him some. He actually seemed much happier with me too. It was like he knew where his place in the herd was (I was firm but not violent with him) and then he didn't need to constantly be fighting for the lead position. He actually went from almost impossible to catch in his stall, to coming over to the door and putting his face in the halter for me :)