Yes, if you have multiple domain names all pointing to the same site using Mollom to protect against spam, Mollom will work automatically even if only one of those domains has been registered to the site on Mollom.com.
In addition, if your installation has multiple subsites that all share the same user table (like a multisite Drupal installation using Domain Access, for example), then a single Mollom subscription registered to one of the subsites will work properly for all of the subsites (as long as all the subsites are using the Mollom module).
Because Mollom uses user data from a site to inform its spam filtering, each site that has its own user table must have its own set of API keys from Mollom.com.