There's two things that may explain what you're seeing.

1. The mites may have left because the lairs were, for a considerable period of time, under the dominion of the player or an AI.

2. An AI army may have killed the mites, but failed to loot the lair, either because it lacked a champion, or because its champion thought there was something more important to do.

the lairs are right next to my starting position with no other AIs even close, and this is turn 10 so I doubt it... Is it possible that other, more aggressive monsters ate the poor mites and did not pick up the treasure? (which would actually be kinda cool...)

Is there any chance you have modded your local xml to try out some of the changelog changes?

I mention it because one of the changes (4 base hp + 2 per level) ends up giving the mites negative hit poitns (with all their hp penalties) so they end up dying on placement, leaving their lairs empty.  I fixed it for the patch by adjusting their hp penalties to fit with the new scale but for some reason it sounds like you are running into the same issue.

Not me. But also I have not seen any more empty lairs.

Poor mites, too sickly to live