I've reported this bug in the recent past and it has reportedly been punted towards the Q&A team. Whether that leads to something or not is up to the ssgods - and they're known to be capricious and fickle beings.
FWIW : my testing involved hitting both favored and non-favored targets with 1d2+11 - 1d2+14 damage in Korthos on an iconic dark hunter and there was no difference whatsoever regardless if I used no weapon (fists) or a 1d2 +1 shuriken. There was no damage change regardless. The screenies of feat selections, character and combat log were sent with the bug report at the time. [with 3 favored enemy feats that is: +6 damage should be *very* noticeable - but there was no difference - tested vs Humans, Monstrous Humanoids and Undead as those were all easily available FE's with easy targets to find].