I agree that clothes aren't everything, they're really only a part of what makes someone popular in high school, but in a way what you're saying proves my point.
You say that nerds don't dress substantially differently, that's not true at all. I'm the son of a fashion designer, so I pay a lot more attention to what I and others wear than the average nerd, so perhaps I can help. Fact is, most programmers dress in clothes that could be at best be described as boring and conventional.
The fact is, if you don't really pay close attention to what people are wearing, stuff starts to look similar, if you do pay attention, you see lots of differences. Programmers generally look at clothes as functional items, they don't get excited at the prospect of owning some awesome piece of clothing.
I tend to buy my best clothes at sales at a 50 - 75% markdown, when they're usually a season or more out of style (so those $230 jeans get knocked down to $80), which is fine by me. Most programmers I've met would consider spending even $80 on a pair of jeans ridiculous. Now, money won't buy you style, I think lots of programmers who try and dress well just end up buying expensive crap, but it can help.
Plenty of stylish people dress cheaply, but doing so takes a lot of time, combing thrift stores and lower priced stores putting together clothes that look stylish buried amidst mediocre clothes. That takes talent and real time and energy.
Point is, style isn't something most programmers do well, because they aren't excited about clothes. If you can't be passionate about something, how can you hope to do it well?