If you hide only one anchor text with any dirty css trick, then it is fine. Such a thing won't impact in seo, unless webmaster main AIM is not about manipulating search ranking.
Search engine bot also use similar webkit like our browser use, so if browser don't see nav link then Googlebot will also not see. But Google sometimes come with different user agent and IP address to check weather any webmaster doing some nasty things or not, like blocking main googlebot and show different things to user (i.e. doing cloaking) so Google sometimes come with different setting. They might come with text based browser as well like lynx, which they said many times in old days, so still they may be use that kind of browser webkit to check cloaking or spamming.
Normally Google don't do anything if only few portion of webpage is change, but when they see totally different things then manually/automatically they gives penalty to webmaster if they think it manipulate their search ranking, but as you said, it is just one anchor text in navbar, so it won't impact in SEO.