Would it be better for me to change my generating php query links to html links if possible? I was wondering if this would help optimize the site for search engines.
It depends on how many parameters you have in your queries... But yes, generally speaking, stripping any special characters like "?" or "=" always helps. Just don't forget about the 301 redirects.
There is an advantage if you're using HTML... It is SEO friendly and can be easily crawled by spiders...
Static HTML tend to rank better than .php pages with a lot of paramaters in the url (e.g. page.php?name=1462&id=400&search_keyword=test&from=__home).