I am using this(Insert PHP Code Snippet) plugin for inserting PHP code in a HTML page.

My Question is by using these shortcodes are there any bad effects when it comes to SEO and page indexing by search engines.

Why I have this doubt is because I am using another plugin to count the words on each page. The page which uses shortcode showing fewer words even it has more words.

So I just wanted an answer for this one.

Thanks