Was it the loss of the Martian atmosphere that decimated their civilization, and was that caused directly or indirectly by the Anunnaki, perhaps from a close approach of Nibiru?

This is all true. This was the downfall for the Martians. The loss of their atmosphere was devastating and they never recovered fully. This was caused by the Anunnaki and the close encounter with their planet and was followed by further manipulation of them and their society. In typical Anunnaki fashion, they sought to not give comfort and restitution but to see what they could further exploit for themselves, and kept these surviving Martians as slaves to do their bidding. And they have been long manipulated by the partners in the Extraterrestrial Alliance, the Arcturians and their robotic Greys, as guinea pigs for genetic studies to see what they could glean from their unique aspects and perhaps use it themselves.