Berners-Lee's design for URLs, etc. is spectacularly elegant and carefully thought through. It's not a good example to illustrate the alleged superiority of "duct-tape programming".
There are different kinds of design, useful in different situations, harmful in other situations. Whipping out small web sites, patching bugs in messy business apps, etc., don't call for great elegance. Seeking elegance would only get in the way. Duct tape wins. On the other hand, remember Gopher? Gopher was a simple, functional predecessor of the web, designed without much insight. The WWW needed the kind of simplicity that you can't get from duct tape.
I think Joel Spolsky implied "duct tape programmers" to be those who are pragmatic and get things done, those who do not try to show off unnecessary techniques but focus on solving problems, those who do not try to play toy problems with all wonderful constructs but solve real problems with simple elegant lines of code.
There are different kinds of design, useful in different situations, harmful in other situations. Whipping out small web sites, patching bugs in messy business apps, etc., don't call for great elegance. Seeking elegance would only get in the way. Duct tape wins. On the other hand, remember Gopher? Gopher was a simple, functional predecessor of the web, designed without much insight. The WWW needed the kind of simplicity that you can't get from duct tape.