The great thing about internet users is that browsing/surfing behaviors evolve rapidly as they learn to do things the more efficient way. One of the things that users now depend heavily on is the search box. Search is no longer confined to Google and more and more websites now offer internal search to make it easier for users to find specific info found somewhere on the site. This is good practice especially from the user interface point of view. However, when it comes to SEO the search box can become a liability.
How is this so?
To be more accurate, the search box itself is not the problem. The presence of a search box on the site will NOT affect your SEO efforts negatively. However, relying too much on the search box to help your users navigate through the website and not paying attention to the link architecture of the site is a sure way to ensure that your site will not be optimised for crawling.
The main thing that is overlooked due to over reliance on the search box is deep linking. Deep linking is a no no for SEO. Avoiding deep linking simply means making sure that ALL pages are accessible and are only a few clicks (preferrably not more than three) from the main page. The reason behind this is that spiders, as we all know, discover the pages in your website by following links. Spiders do not always crawl all the links and the “deeper” (more clicks away from the main page) the page is the chances that the spider will overlook it increases.
So if you want to use a search box by all means do so but always remember that search engine spiders use a different way to crawl your website, and make sure to pave the way for spiders to do their crawling without any snags.