No, the black orbs can not nullify the effects of genjutsu.
The chakra is highly malleable, able to be shaped into various forms for different uses, such as a barriers, protective orbs, and most commonly, a staff with an incomplete circle. With his complete control of the Ten-Tails' power, Madara can also apply the Yin–Yang Release to nullify all ninjutsu it comes in contact with - Naruto wiki
As genjutsu is not 'touchable' it would be impossible to touch the genjutsu with the orbs. Then again this is not necessary to begin with.
Members of the Uchiha clan can break or see through genjutsu using their Sharingan
Knowing that he even is a step beyond the regular Sharingan we can safely assume the he would just use his visual powers instead of the black orbs to block/cancel genjutsu