In case someone bumps here again, I found two ways it can be achieved within a theme without using any using module.

 1. Using custom CSS:

    .user-logged-in .menu.menu--account a[href="/user/register"] { display: none; }

 2. Using custom JS:

    $('.user-logged-in').find('.menu.menu--account a[href="/user/register"]').hide();

This is applicable only if you are [customizing your theme][1] in any way.


  [1]: https://www.drupal.org/docs/8/theming-drupal-8/adding-stylesheets-css-and-javascript-js-to-a-drupal-8-theme