I don't know if the lair system's resources (ie: raw rubies, copper, pools of acid) are set to spawn in the Lowerdark but I've never run into any. If they are spawning down there I'd suggest upping the number of locations they can spawn in, or the frequency.
I've always loved the idea of a lair in the Lowerdark, it's a chunk of the server I think is really cool but doesn't see much love. Putting some resource spawns down there would really expand monster PCs options when it comes to establishing a lair if they'd be willing to risk the super dangerous spawns.
This may no longer be the case, but in fact when lairs were a new thing I had heard from lair masters that the staff specifically didn't want them placing their lairs in the Lowerdark.