I use pecan almost exclusively, and I've never purposely de-barked. If it falls off, I discard it. I've noticed no ill effects, but different woods may have different properties, as several have pointed out.
Weber Smokey Joe
18" Weber Kettle
22" Weber clone kettle
Curb-foundling char-broil gasser
WSM: Assembled! First cook: 8/25/06
Fanatical devotion to the Q