The free-hit rule is more recent than Duckworth–Lewis so the original D/L method (which came into force in English domestic cricket 1997) would not have taken this into consideration. I have been following cricket for many years in England and I’m not aware of any changes to the D/L system taking the free-hit into account.
However, it is worth noting that Duckworth–Lewis does take into account wickets lost by the batting side: the more wickets you lose, the steeper your run chase will be. If you have a free hit, you are less likely to lose a wicket; this in itself should be a slight advantage to the batting side, even if Duckworth–Lewis does not consider free hits in its calculations.
