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For one thing, the SE's don't give as much weight or credence to information beyond 100KB (some think it's 100 links but I see no evidence of that). So links far down in the code won't have much value/impact.
Equally important, the more links you place from your homepage to internal pages, the more the homepage's link juice is divided into smaller increments, and that's not necessarily a good thing.
You need to think about what are the very most important subpages in your site (usually akin to internal 'hub' pages or nodes that cover a specific topic) and limit your links to those pages, plus perhaps a handful of very important deeper pages.
Have a look at BT's classic on Themes [webmasterworld.com]. Read the entire thread but pay particular attention to the fourth post; the one that includes the graphic.
As for simply getting pages crawled, that's what sitemaps are for. ;-)