Eben is correct in his answer. It's unnatural to only link to a home page or to an individual page for a specific keyword phrase or any links at all.
In my experience, cannibalization is a false flag concern for the vast majority of sites and it's overplayed by some people in the industry when there are so many other things to be focused on that have a higher value. I say this because it's like this. If your site is really well designed and people can easily navigate to find what they are looking for, then you should be happy for either your home page OR an inner specific page to be found and clicked. And when you execute properly with a mix of targets (home and inner pages), you will ultimately get BOTH the home page AND the inner page to show up in the search results.
Having said that, burying links in the footer the way you describe is NOT an SEO best practice. First, because footer links are the lowest form of link you can have on a site. Second, it's a signal that you're potentially attempting to spam the search engines.
If you wish to continue to maintain links in footers it should not be a case of keyword stuffing attempts, but instead, links to highly important pages where the anchor text is not specifically a keyword phrase, but instead, a description of the link destination. And typically, it should be a mirror of the main site navigation, or alternately, to second tier corporate pages (such as customer service, privacy, disclaimers, etc.).
On a final note, I'll suggest that you can ultimately only truly optimize the home page for the site's highest level topical focus or intent, and secondarily, to whatever other keyword focus you have actually optimized the home page for. So while it's okay (and natural) to have links pointing to the home page that have anchors with other keyword phrases, the majority should not be so.