You should disable and uninstall modules that you don't need. It is done in the following way:
- You disable modules by deselecting the relevant check boxes in the module list, and then saving the settings. This turns off any functionality provided by the module, but won't delete any data. If you enable the module again, everything is restored.
- Modules are uninstalled at the uninstall tab found at the module list. Uninstalling a module removes any data saved by the module.
There are some benefits of removing unnecessary module folders from your file structure. The biggest benefit being that you won't confuse other developers with modules that are neither used nor enabled. You cannot remove the files using Drupal's web interface, but must manually go into your Drupal files and remove the module's folder at sites/all/modules. You should always uninstall a module before removing its folder.
Note: This step is often overlooked and undervalued. This is a mistake should you grow your new site to be a great success. Don't miss this step for your peaceful future.