Freemasons on this planet do not currently recognise any Grand Lodges or Masonic obediences of a non-Earth origin. Hence we are not in Amity with any Extraterrestrial Masons, and if there is any Alien Masonic activity happening on this planet it would be considered “Clandestine”: i.e. if a regular Freemason tried to take part in it, he would be subject to Masonic Disciplinary Proceedings.
Furthermore, if an extraterrestrial applied for membership of a regular lodge here on Earth, it would run into problems. The qualifications for membership are to be a free *man* aged twenty-one years or more, who believes in a Supreme Being. Hence there might be arguments over whether the extraterrestrial can properly be said to be a “man” or not.
More prosaically: Freemasons probably do know the truth about Extraterrestrials, as many of them (Freemasons that is) are intelligent men who keep up to date with current thinking on astronomy. Freemasonry itself does not have an official opinion on the matter.