· Doing so will make it complicated, difficult or near impossible to apply site updates such as Security and bug fixes.
· You will make it difficult for those that come after to maintain the site.
· You could possibly leave your site vulnerable to exploits.
The Drupal core has been designed to be modular, so there should be no reason to hack it. If there is a feature you want and it cannot be accomplished outside of modifying core, consider submitting your hack as a patch. Create an issue and tell the community the feature you want to accomplish. It will then be tested and your feature may become a part of the Drupal core.