Does Ganon "recognize" the Yiga Clan? No.
According to the Zelda Wikia, the Yiga Clan was not necessarily formed to follow Ganon - it was formed due to the hatred towards the Hylians, to which they pleaded their allegiance to Ganon.
(emphasis my own)
It is revealed by the Sheikah Cado that after having proved to be key in sealing Calamity Ganon 10,000 years ago, the ancient Sheikah technology was at first praised as the power of the gods. However, the people of Hyrule began to fear their technology as a threat to the kingdom. As a result, the Sheikah became outcasts and lived in exile. Although most Sheikah chose to cast off their technology and live simple lives, others fostered hatred towards the kingdom of Hyrule for shunning the Sheikah despite all they had done for it, leading them to swear allegiance to Ganon. This resulted in the creation of the Yiga Clan, who dedicate themselves to eliminating all who stand against Ganon.
100 years before The Great Calamity occurred, the Yiga Clan tried to assassinate Zelda in order to prevent the future sealing of Ganon again.
According to Zelda's Diary, it is revealed the Yiga Clan were active 100 years ago shortly before the events of the Great Calamity. At one point, the Yiga Clan attempted to assassinate Princess Zelda before she could awaken her sealing powers which were a great threat to Calamity Ganon's return.
So to reiterate your question, Ganon does not recognize the Yiga Clan, but the clan members will do everything in their power to ensure Ganon's return and the destruction of Hyrule.