I would definitely not use no-follow, that just doesn't make any sense as your navigation links are part of your link juice to those pages.
Also, no-follow is meant for links that are outside a webmasters control or for paid links so they are not intended to be used by a webmaster on his own site linking to his own content.
As for too many links in the navigation (at least that is what I assume you meant), that indeed can be a problem for useability. It is always a good idea to see how well-known brands handle this problem, so have a look at for example http://www.ebay.com/ and http://www.amazon.com/
By not showing all links directly in the navigation you can have both a more user friendly website and get rid of the issue you think you have with search engines as then you can better funnel the link juice to the more important pages.