For internal, we calculate internal PageRank. We use some basic natural language summarization to compare pages. We do the basics, like check for redirect chains and busted links.
For external, this isn't so much a technical issue for us as a management one. We check for redirection and 404s, but can't do much else.
But so many folks neglect the technical aspects of internal linking. We see redirect chains, missed hub opportunities, etc. Your site is its own best source of links. On the other hand, remember that a technical SEO audit shouldn't become a UX audit or an architecture audit. Focus on consolidation and on-page linking, not high-level site architecture (unless you're asked to).