'You' may be three deep but the spider (or any other agent/person without the requisite permissions) has no clue what the directory structure is above the folder that is mapped to the root for your web site. So that argument is not much of an argument IMHO either in favor of or against folder structure being n levels deep.
Three deep from what? The DocumentRoot for most of my sites is something like /home/domain/www/, so I'm three deep before I even get to index.htm.
Folder structure appears to have no bearing on whether a spider will crawl the page or not. If it did, all those URL rewrite programs would be doomed. They add a slash for every parameter and make it appear as though there are no question marks in the URL and that the URL is static. They seem to get spidered just fine and the spider has no clue that there is no existing folder structure that matches the URL.