It sounds to me like you need to do a Content Audit with the goal of pruning out all pages with zero traffic and zero links from the index. See the following resources:
How To Do a Content Audit - Step by Step (Moz)
Classic Content Audit Articles (Linked-In)
Content Audit Case Studies (Linked-In)
Using URL Profiler for Content Audits ( URL Profiler)
Here's the slide deck for a presentation I gave last year about them.
Here's a recording of a webinar with the presentation above.
Common Content Audit Strategies I think the site you described would be considered Extra Large with a Penalty "Risk" so this is what the tool recommends:
"Focus: Prioritization of Pages for Content Optimization. Are you SURE there is no content-based penalty risk?
Most sites with this many pages have major content issues, meaning this would be the wrong “situation” for them. In the rare case that they don’t, prioritize the pages based on rankings, traffic potential, revenue… and propose how many to improve each month with ongoing copywriting and on-page optimization."