Does Google crawl Drupal sites in maintenance mode? I'm using Aegir to clone copies of my site under a subdomain name ie test.mydomain.com. 
These copies are in maintenance mode to keep away spammers and prying eyes. 
I then use these copies to carry out tests and development work before committing changes to my main site mydomain.com

But am I hurting my SEO by the existence of these cloned sites? Does google crawl a sites which has been put in maintenance mode? Will it penalize me for having so many dead end subdomains?
When you put a Drupal site in maintenance mode, non-administrators see the standard maintenance mode page (assuming you clear caches after doing so).  If you examine the response, you will see that it is sent back with a HTTP status code of 503, which from RFC 2616 is:


  503 Service Unavailable
  The server is currently unable to handle the request due to a temporary overloading or maintenance of the server. The implication is that this is a temporary condition which will be alleviated after some delay. If known, the length of the delay MAY be indicated in a Retry-After header. If no Retry-After is given, the client SHOULD handle the response as it would for a 500 response.


And from the Official Google Webmaster blog:


  If my site is down for maintenance, how can I tell Googlebot to come
  back later rather than to index the "down for maintenance" page? You
  should configure your server to return a status of 503 (network
  unavailable) rather than 200 (successful). That lets Googlebot know to
  try the pages again later.


So, that gives evidence that Drupal does the right thing, and that Google will revisit your site and index pages the next time it gets back a non 5XX status code.