In D&D it appears that "to wield" means to "attack with", not simply "to use". It's definitely a poor choice of wording that could have been defined more clearly.
In general terms, a combatant dual wielding an axe and dagger is clearly using and wielding both weapons, even if he can only attack with one at a time. Note: "in general terms", rather than by rule terminology.
I am quite sure that the intent of the rules is that a rogue only gains +1 to hit when making an attack roll to see if he hits with a dagger, and only gains a die-type increase to shuriken damage. I don't think it's quite as clear as some people are claiming, however, and I'm willing to give the benefit of the doubt to people who may have genuinely believed "to wield" in this instance didn't specifically refer to making attack rolls for that weapon.