Modules that have never been enabled are not a performance issue.
The issue report you linked is referring to what Drupal does when it doesn't find an enabled module; in such case, Drupal rescan the directories where the modules are placed, causing performance issues. To avoid it, modules should be uninstalled from the module page, and then deleted from the server directories; if you do this, you will never have any performance issue.
If you are thinking of removing the database rows found in the "system" table referring to those core modules that you don't use, then it is useless, as Drupal adds those rows back every time you visit the module page.
If Drupal were not doing that, you would not be able to install new modules. When you visit the modules page (admin/modules in Drupal 7), Drupal rescans the directories where modules are placed, to list the new modules you could have copied on the server. If it finds a module that doesn't have a row in the "system" table, it adds it; it cannot know if you removed that row from the table, or it is a module that you copied on the server, and you want to install.
If you are thinking of removing the module files for those core modules you don't use, you should keep doing it every time you update Drupal; as there isn't any gain, it's useless doing it.