Google and the other search engines have improved their algorithms over the years and now use hundreds of criteria to rate the worthiness of a website. Unusual patterns raise sp,e doubt about the worthiness of a site. For example, a quality site, with naturally gained links would not normally have mostincoming links to their homepage. Naturally obtained links tend to point to a wide range of internal pages along with homepages.

Lets face it, you probably have enough home page links already. Deep links will help make your link building efforts appear more natural.

You cannot and should not have your homepage optimized for more than a couple of keywordphrases. Ideally, your SEO efforts should included internal pages optimized for different keywords. Internal directory links will help your search engine rankings.