I suggest the following things to make Shadow Lairs more profitable (i.e. worth running for any reason other than crafting Shadow Lair gear):
1) Remove heat drops from them entirely. The vast majority of the people running a Shadow Lair aren't going to be using the effort to heat gear. Replace these drops with crowns.
2) Double the crown earnings. Replacing heat with crowns may accomplish this already, but crown drops will probably need to be further increased anyway.
3) Increase the chance of gear drops from treasure boxes significantly (to average 1 drop per run).
The reason Shadow Lairs aren't worth doing on a regular basis is because you have to do Shadow Lairs in order to get the reward from them (or pay an exorbitant 4k CE unbind fee on shadow gear). And the crown earnings are meh. There's really no incentive to do them. Increase the earnings so that they're at least on par with FSC and perhaps slightly better and people will be more inclined to do them on a regular basis (and buy more keys).
+1
I haven't been to the Shadow Lairs yet, but from what I read on these forums, this might solve the problem in a simple way.