As a SEO consultant I wouldn’t recommend this method of hiding navigational elements with just CSS as they are still present in code. This will create what Search Engines refear to as “hidden links” and that will severely affect your possiblity to rank well.
Hidden links will also end up in the category of displaying different content to the users then to the Search Engies and that will make it a dubble penelty rule breaker.
Also remember that a main navigational element will be present on all URL’s on your entire site and by that downrank all your content as the penelty counts per URL basis.
Sure, effect of site wide links has gone down abit, but is mostly the effect of them from a possitive count and makeing it less needed to prevent link juice leakage from site wide links (like footer links), but the negative effect of penelty from creating site wide links are still there.