Their eyes popped out on their own with the crushing chest injuries..Eyes do that with extreme internal pressure.. They have been known to pop out even with a strangling..
It's an interesting point i haven't heard before. But Nicolai would have experienced the greatest skull pressure and his eyes stayed in place. Another theory for the damage to Semyon and Lyudmila is that as the meltwater made the bodies mobile they stayed frozen at the head, eventually detaching leaving "bits" behind. still frozen into the ice.
As for the injuries, the evidence points to being crushed under the snow (no bruising). There's lots of possible causes, my favourite is a slab slide due to unnaturally high temperatures. If you look at the photos of the den after being dug out the side of the snow "wall" behind the man sanding there looks like "settled rubble" = avalanche/slab slide?