I'm not sure if lumping Zappos (1500 employees) with GitHub (100 employees) makes much sense. I don't believe the organizational structure has an impact until you get over a few hundred employees.

It's kind of like sports. If you are playing in a niche sport that only has 3 teams then you don't really need committees to maintain the rulebook, a referee union, a centralized body to represent the teams or a players' union.

When you're small enough everything just either works or doesn't. The owners of the company are personally involved, you feel responsible for the success and there's a great deal of transparency.

With that said I do believe most smaller companies should be flatter, and that it starts at the top, like not having a CTO, CIO, VP Technology, Director Technology, Director of IS for a 20 person company.