Some kids who are nerds might be bullied. But that doesn't mean that all kids who are nerds are bullied nor does it mean that being a nerd is the sole reason they are bullied - some nerds aren't bullied. Some fat kids are bullied, some fat kids aren't bullied. Some rich kids in poor schools are bullied, some are not. Some poor kids are bullied, some are not. Some kids with braces are bullied, or red hair, or gay parents, or who play musical instruments, or who are short or tall, or who are sexually active, or who are not sexually active, or any host of things. And you know what? Yes even cheerleaders and athletic kids get bullied - plenty of cheer squads, etc have mean-girl vibes going on with one girl within their group being the scape goat.
Usually kids who are bullied have something different about them, but often times its something random and not all that different. There are many reasons why a kid might be bullied and sometimes its not even about the victim as much a its about the bully himself.
I think to say "being a nerd = being bullied" is ridiculous, and to imply being a cheerleader or the like means no bullying ever occurs is dangerous. Does it happen that sometimes some nerds are bullied? Of course it does. But that doesn't mean it always does, or to all of them, or to only them. Because it doesn't. Bullying is something that can and does happen to all sorts of people.
OP's son was bullied - I don't doubt it if she says its so. But no one knows for sure, not even her or him, if it might have happened even if he didn't do better then his classmates academically. He might have been picked on no matter what. He might have initially been targeted for saying the wrong things, or for not liking something popular, or looking different and the fact he's smart was simply tacked on as another and easy to spot thing to focus on. The only ones who know exactly why the OP's son was bullied are the bullys - and they, as children, might not even clearly understand why. If it was more then one kid bullying, many might have simply been following the herd.
Having a "dress up" day is a way to encourage kids to be excited about going to school. A way to make school fun. will each theme work for every kid? Of course not. But its important to look at the bigger picture - if kids who think school and doing well = uncool can change, even a tiny bit to think school is awesome even in just a small way, that's overall helping the situation of an academically struggling school.