If the user knows what a site does and what they're trying to do, then it makes sense to have a really clean design that gets them where they're going in the fewest clicks. But back in 1997 most of eBay's prospective users didn't know what eBay was, what they were doing there, or what eBay could do for them.

Hypothesis: The less the users know what the site does and what they want to do, in other words the less clear the goal, the less important it is to minimize the number of clicks to reach that goal. And the more experience users have with a site, the more important it is to streamline the process.

I think premature optimization applies to not just code but also design. For example, joining the Wikipedia community is probably much more difficult now even though the meta pages are much more ordered and clean than a few years ago. Whereas when the community pages were a hodgepodge of random crap it was a lot easier to just jump into the community and start contributing.