Yes, chimneys do get struck by lightening.  A lightening strike to a chimney can cause a significant amount of damage.  
That damage can affect the structural integrity of the chimney.  In this case on Marlborough St., in Boston's Back Bay, the force of the lightening strike sent brick flying down to the street and through someone's skylight.  Always have your chimney inspected after a lightening strike.  Even if it looks ok, best to be safe.