There's this thing where guys are made to believe that women like it when you compliment their shoes. I've seen it happen in films, TV show episodes, so guys are probably just using it without thinking about that much. Ask him what he exactly likes about them and he may need to improvise, which will be noticeable.
It could also be that he's looking to compliment you based on something that's not sexual (butt, boobs), so shoes are suitable, but so is hair. Like the other answer states, complimenting the eyes is a bit cliche. In that sense, the stuff on movies and on TV are somewhat right, but if it really works, I'm not sure? What if she's wearing normal, worn down ballerinas... can't really compliment that, can you?