Think of deep links as the platform that holds up the rest of your site (in search engine terms), without deep links your site is going to fall. I think someone mentioned about hosting different sites on different servers.. that is very true but Google also checks WHOIS information too.. so if you're running many sites that link to each other, make sure you're not named on the registry data.
Just wondering, what should be the ideal % of home page versus inner page optimization? Seems like it's pretty hard to rank up inner pages without keywords in URL.
Build links to all parts of your website. Especially to your homepage and important sub-pages. Use different anchor texts and use different methods of link building.
It depends on your site as well. If you are selling then it might be good for people to go directly to the sales page for example. However if there is important information on your home page that prospective buyers need to see, then it might be best to concentrate on link building to the home page.