There are two types of people in this world, browsers and searchers.
You see the search box and type in what you want and then look at the results. The results are based purely on your input. The thinking involved is primarily about what to search for. Different search phrases will yield different results. The amount of clicking is minimal and the system doesn’t need a hierarchy. The down-side is that you may need to search several times to find just the right keyword. Sometimes one search phrase is dominated by results that are not what you meant.
Browsers are different. They like to narrow down their choices by clicking on a general link and progressively getting more detailed. Each link down is more specific until you find your result. Browsers do not like a million links available all at once. They like to have simple choices and each one is splitting the result set in half. They don’t want to think about input, they want you to give them 2-5 simple choices and they will narrow down from there.
Of course, no one is just a browser or a searcher. I am searcher with general web information (Google), but a browser or many other kinds of systems. Generally, depending on the system, I am either one or the other.
As a designer, you have to understand that the world is filled with different kinds of people. You shouldn’t diminish browsing because you have a search box or vise-versa. The most important aspect of a designer is Empathy. You have to feel what it is like to want to search differently than you do normally. You have to see all of the different and perfectly valid world views.
One of the hardest design tasks for the browser audience is to figure out the information architecture / taxonomy. Some items belong in more than one or or none at all. In my experience, there is always a way to work it out. Just make sure that each level has clear and unambiguous choices.
I find that many designers and certainly many business drivers make assumptions about their audience that don’t match up to reality. Do a good job with your assumptions and you will gain real-world benefits from your website.