If your commute isn't hilly and doesn't have many stops, the extra bike weight won't make too much difference on the road...it might feel a teeny bit sluggish pulling away from a stop but it will be fine once you get up to cruising speed.

As for the racks versus a bag, it depends on how heavy your cargo is. If you're carting a lot of baggge, you'll find it a lot easier to ride with the stuff on a rack.