Robert_Charlton - 5:25 am on Apr 1, 2013 (gmt 0)
Wasn't there a quite recent thread asking the exact opposite question: Do search engines prefer a shallow site layout where everything is-- or appears to be-- in the top directory?
Here's the discussion that seemed to ask that question, but in truth the poster confused so many issues that he wasn't accurately asking any one question....
Should I flatten my store's URL structure for better SEO?
helen's question might be making similar conceptual errors as the original post, but the emphasis is in a different area.
helen... the above post is going to be tough reading for you, but I suggest you try to make sense out of it. You're not apparently asking about multiple file paths, though... the part you're asking about is direct links from home vs a hierarchical nav (navigation) structure.
Note, and this is important, that nav structure and url directory structure are not necessarily the same thing. Sometimes they are, but nav structure is about clicks from home... which can be independent of directories.
Also, it's not the size of the site that matters... it's the number and quality and relevance of inbound links in relationship to the structure of a site, the quality of the content, and how well that content engages search visitors. But large, well known sites generally can do things that small sites can't, and you need to be aware of those differences.