In Drupal 8, you cannot anymore disable modules. You can only uninstall a module, but in the case of the Comment module, you first need to remove any Comments field. In fact, on /admin/modules/uninstall you will see the following message:
The following reason prevents Comment from being uninstalled:
- The Comments field type is used in the following field: node.comment
By default, the Comments field is added to every content type.
Once you remove that field from every content type, you will be able to uninstall the Comment module from a Drupal 8 site, if there isn't any module that depends from the Comment module. Otherwise, you first need to uninstall first those modules.
As for updating Drupal, updating Drupal doesn't install the core modules you previously uninstalled, not even the ones the profiles you used to install Drupal would install.