Most search engines find new pages by crawling links from other sites. At the same time, the more links to a page and the quality of the pages linking to a page, drives the quality of the page being linked to. These are all basic SEO principles.
This is why many SEOs place links to their most important internal pages, right off of their home page. Why?
(1) They want them indexed faster and typically one's home page is indexed more often than other pages (not always). So having a link from your most popular page to other pages, help the other pages also get indexed faster.
(2) Also your home page normally has the most amount of links to it, so typically has the higher link equity of all your page (not always), so linking to pages off your home page will funnel some of that high link equity to the pages you are linking to. This may result in a higher ranking for those pages linked to from your home page.
Again, all basic SEO principles.
The myth is having pages based in the root directory of your server results in higher ranking. That is not true, it is all about the click path.
That being said, does it ever make sense to require people to click and click, five or more times to get to an internal page? Since search engines will have to do the same clicking, it might take them longer to find the page and it won't pass the majority of your home page's link popularity.
JohnMu, a Googler, in the Google Webmaster Help forums discussed just that in less than a sentence. He said:
I'd have no problem clicking through 5-6 links to get to highly specific content if I needed it and your site had it.
Google knows that there is a logical site hierarchy. Google knows that there are deeper pages on a site that is important. As an SEO, it is not just about linking to them off your home page, but also about getting external links to those pages. And it is also about utilizing your other internal pages to get the search bots to bite them.
Forum discussion at Google Webmaster Help.