We have news of a fairly new Star Trek mod for Homeworld 2, which has an alpha version available for download as of August 2011 – here is the official synopsis of the mod:
Homeworld 2 meets Star Trek: Armada 2. Set in the 2380′s you will find three superbly balanced factions to face off one another, the Alpha Quadrant superpowers! The versitile United Federation of Planets, the formidible Klingon Defence Force and the enigmatic Romulan Star Empire.
Visit their ModDB page and download the alpha version of the mod at http://www.moddb.com/mods/star-trek-continuum