In which case, it's subtitle would become (2013), which is unlikely, since it would be confusing, since it's set in the 23rd Century
It wouldn't be a subtitle, it would simply be included on a removeable sticker on the home release packaging (usually located on the top edge). An example would be "The Punisher (1989)" and "The Punisher (2004)." Both films had the exact same name and no subtitles. The same was true for "Crash," "Heaven Can Wait," and many other films with duplicate names.
If the next film is simply called "Star Trek" again, it is unlikely that people will confuse it with either Star Trek XI or TOS if they go into the theaters in 2013. Fandom also won't be confused as they'd call it either Star Trek XII or Star Trek 2013. In addition to the aforementioned label sticker on the home video release, Star Trek XII will probably have different cover artwork from the previous movie.