I will take your advise Ryan. The one site with numerous links was getting a little ugly so I'll let the navbar work for awhile and see what happens. Up to now people tend to find this site through long-tail keywords so the links in the sidebar is a moot subject as far as navigation.
All those warnings spooked me. When I built my first site many moons ago with Dreamweaver and even Frontpage there were tests built in to the software to analyze the site for broken links and a visual of your navigation.
My main site is that old and my linking system worked fine. If this was a real problem wouldn't an extensive sitemap be a problem? That could potentially be link loaded.
And you're absolutely correct - if they are helpful to the users than don't remove them - I always concentrate on ease of navigation for the user and page load speed. If you can't retain the visitor all the links in the world won't help or hinder.