In the Einstein example above, I don't have any trouble believing that there could be a ship named Einstein
as well. Starfleet presumably manages the names of its ships, and ensures there are no duplicates, but things are probably a little more lax with shuttlecraft names. There are probably so many shuttlecraft that you're going to have repeating names across different motherships. In the Starfleet records, a shuttlecraft is probably just known by its registry, eg - NCC-1701/7 or NCC-1701-D/15, and then perhaps the name is actually assigned by the ship commander, as scotpens
mentioned above. (IIRC, one of the Titan
novels showed this happening in the TNG era too.)
As an example, in the 24th century shows, both Cochrane and Goddard appeared as names of both starships and shuttlecraft. I'm sure there are other examples, too.