I noticed that in the new (2009) Star Trek movie, somebody called one of the shuttlecraft Mirata. That is way too close to be a coincidence, right?
Marathon was making a shout out to some episode of star trek with a shuttle with that name, and the movie features that shuttle. This seems unlikley, because I haven't been able to find anything related to "Star trek shuttle mirata".
Possibly, somebody on the production team slipped the name into the script at some point ("I need a name for a shuttlecraft, anyone?") as a shout out to Marathon.
The third, least fun possibility is that it is in fact a coincidence. But of all the pretty sounding names, why that one?