Does Google’s Algorithm Factor In Links On Indexed Pages Alone Or Non-indexed Pages As Well?

In episode 135 of Semantic Mastery's weekly Hump Day Hangouts, one viewer asked whether Google's algorithm factors in links on indexed pages alone or on non-indexed pages as well.

The exact question was:

Hey there, kind of a newbie question but here it goes –
When looking at your anchor text profile as a whole, does Google's algorithm only factor in links on indexed pages or non-indexed pages as well?

This question became very important for after I realized that the majority of my Web2 links were not indexed. (I built these primarily to balance out the anchor text)