Hello,
In some sense Smagorinski is like Large Eddy Simulation (some specialists will deny this but they are free to give us explanations...). So its efficiency probably depends on the mesh refinement. Having a different model on the vertical is a bit schizophrenic, as we have an assumption of isotropic turbulence behind Smagorinski and k-epsilon (hence "model best understood in 3D"), anyway it is true that with aspect ratios of sometimes a factor 1000 in our applications it is difficult to claim that turbulence is numerically isotropic.
Regards,
JMH