I know it is ideal to keep your file structure as flat as possible for the spiders. Does that mean your link structure or the physical files in your wwwroot diretory? For example: wwwroot/articles/a/whatever/article.html index.php links to article.html So article.html would be 1 link deep right? Not 3 deep like it is in the wwwroot directory.
Keep your site map in the root up to date and try not to nest too deep. Make sure all the internal links work and keep an eye on the external ones. SE spider bots hate broken links.
What exactly do you mean by too deep. For example: index.html links to page1.html links to page2.html links to page3.html links to page4.html So page4.html is 4 links deep. So what if index.html links to page4.html? Then it would only be 1 link deep right? What if you page4.html is in the directory: root/articles/one/two/three/four/ Does that effect anything?