It will make a difference in crawls and indexing, which for purposes of this discussion is the point of using it in internal navigation.
Nope, not according to Matt Cutts, in numerous quotes and interviews he's done. What Matt says:
1) For Google, nofollow'ed links are completely dropped out of their link graph.
2) Google doesn't even use nofollow'ed links for discovery.
3) The nofollow meta tag does the same thing as rel="nofollow", but at the page level instead of the per link level.
Matt discusses it in some detail in a video at the Webmaster Central Blog [googlewebmastercentral.blogspot.com].
[edited by: Marcia at 6:12 pm (utc) on Dec. 6, 2008]