Since the latest DLC launched, I have had two games where one of the AI factions has just disappeared (all systems suddenly vacant, home system sitting there untouched) and the usual xxx has been defeated message has come up.  Both times was fairly early in the game, last one UC were not playing.  Is this a new method in taking out an opponent?  Admittedly, I am fairly new to the game (started playing last summer) and still learning my way around the game, but I found it odd that the opponents just winked out so quickly.

Sometimes AI can be eliminated by bankruptcy. Could you share a save so we can take a closer look?

They could also have been killed off by a rebellion after someone hacked their homesystem. This is actually a really strong hack, if the hacked faction does not already have a military fleet, and a good reason to not leave yoour homesystem unprotected from hacks in the early game.