Done properly, there is no disadvantage to siping tires, only advantages. Properly siped tires run cooler and they typically actually last longer. Many factory tires come siped from the factory and they certainly would not sipe tires if it could cause problems for the tires.
The only real caution is if you do have your Mud Terrain tires siped, which typically have four tread blocks across the face, is to only sipe the two center rows of tread blocks. For rock crawling and other extreme level trails, that leaves the outside tread blocks unsiped to leave max strength where it is needed the most.
I've had two sets of MT style tires siped and really liked the results.