Theme overrides for custom hook_theme() in Drupal 7
This should happen automatically. Most core modules define theme hooks which you wouldn't think twice about overriding in your theme. Take a look at node_theme for example http://api.drupal.org/api/drupal/modules--node--node.module/function/node_theme/7.

The devel themer module should help you out with such things. Needs some work for D7 but should help.