Hi,

I think that your site will be affected, not because of Joomla, but because you will have other links.
A strategy could be to create a copy in Joomla and verify before put online the site with Joomla all links to your site, see which pages was linked and try to create redirect to new page with same content.
Then also be sure that in Joomla you will use SEO links, I know there is a module for this.

See more about redirect on
www.mcanerin.com/EN/articles/301-redirect-apache.asp and http://httpd.apache.org/docs/2.0/mod/mod_alias.html

Hope this help.