Web Crawlers and shortcode.

If my pages have a short code [xyz] with no parameters what does a search engine or a email harvesting bot see when it crawls the site?

Are bots able to force expansion of short code or do they just see the literal short code?

Also, I am in the process of locking down my website with .htaccess files. What folders do the search engines need to have access to? Will .htaccess files stop robots?