Because you can replace/remove all kinds of things, you can potentially break your site. It is not wise to replace words like 'html', 'body' or (parts of) words that are used in inline scripts.
However, the cool thing is: all replacements are not permanent. They are done on-the-fly. So when you turn off the plugin or remove the replacement, your website is back to the original state.
Also, there are many useful features and settings enabling you to search only in certain areas (for example without touching fragile areas like html tags and outside the html body), as well as assigning replacements to certain conditions (for example only specific user groups, or certain seasons, or specific extensions).