Yes and no. PB2 will not recognize objects that were created with version 3 as Profile Members so the PB2 quantifier tool will treat PB3 objects as normal SketchUp groups and components.
The PB2 Quantifier Tool can still report quantities and costs for PB3 objects but the accuracy will not be as good as the Quantifier Pro plugin since PB2 will not be able to determine the length of the object based on the path that was used to create it.
Quantifier Pro is a big upgrade from the PB2 quantifier tool and it will only continue to get better. We highly recommend you check it out!