This rogue suffers from no being able to APL appropriate encounters. This a problem with the rogue at higher levels. They lack the ability to hit well. This rogue will probably miss with half their attacks. This will just get worse as time goes on. By level 12 they will be maybe hitting 1 in 4 attacks.
So this will go one of two ways. A single monster encounter which the rogue can't hit. Or multiple less CR creature that the rogue can hit but they will be at risk due to the low AC and Hit Points.
This rogue is too focused on stealth. They could have better to hit chance, better AC and better hit points with more rounded build.
Any suggestions for creatures that are immune to Non-Lethal damage AND are not undead?He can just deactivate the Merciful ability if he runs into such a thing.
He can, sure, but he'll be burning two turns to turn both weapons off. Merciful is a command word effect, and command words are a standard action to activate.