It would be keen if Drupal core were nice enough to alert you if you tried to register a module and theme of the same name... but it doesn't.
If you name your theme and a module the same name you get name space collisions. E.G samename_block(..) will conflict if you have it declared in both module and theme.
It would save a lot of new Drupal developers frustration if Drupal didn't let you register a theme and active module by the same name.
Also noted here http://drupal.org/node/143020